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Wang Z, Zhang H, Xiong Y, Zhang L, Cui J, Li G, Du C, Wen K. Remediation mechanism of high concentrations of multiple heavy metals in contaminated soil by Sedum alfredii and native microorganisms. J Environ Sci (China) 2025; 147:179-188. [PMID: 39003038 DOI: 10.1016/j.jes.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/05/2023] [Accepted: 10/05/2023] [Indexed: 07/15/2024]
Abstract
Pollution accident of nonferrous metallurgy industry often lead to serious heavy metal pollution of the surrounding soil. Phytoremediation of contaminated soil is an environmental and sustainable technology, and soil native microorganisms in the process of phytoremediation also participate in the remediation of heavy metals. However, the effects of high concentrations of multiple heavy metals (HCMHMs) on plants and native soil microorganisms remain uncertain. Thus, further clarification of the mechanism of phytoremediation of HCMHMs soil by plants and native soil microorganisms is required. Using the plant Sedum alfredii (S. alfredii) to restore HCMHM-contaminated soil, we further explored the mechanism of S. alfredii and native soil microorganisms in the remediation of HCMHM soils. The results showed that (i) S. alfredii can promote heavy metals from non-rhizosphere soil to rhizosphere soil, which is conducive to the effect of plants on heavy metals. In addition, it can also enrich the absorbed heavy metals in its roots and leaves; (ii) native soil bacteria can increase the abundance of signal molecule-synthesizing enzymes, such as trpE, trpG, bjaI, rpfF, ACSL, and yidC, and promote the expression of the pathway that converts serine to cysteine, then synthesize substances to chelate heavy metals. In addition, we speculated that genes such as K19703, K07891, K09711, K19703, K07891, and K09711 in native bacteria may be involved in the stabilization or absorption of heavy metals. The results provide scientific basis for S. alfredii to remediate heavy metals contaminated soils, and confirm the potential of phytoremediation of HCMHM contaminated soil.
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Affiliation(s)
- Zihe Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Han Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Ying Xiong
- Beijing Water Science and Technology Institute, Beijing 100044, China
| | - Lieyu Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Jianglong Cui
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Guowen Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Caili Du
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Kaiyang Wen
- School of Architecture and Civil Engineering, Chengdu University, Chengdu 610106, China
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2
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Mmbando GS. The link between changing in host carbon allocation and resistance to Magnaporthe oryzae: a possible tactic for mitigating the rice blast fungus. PLANT SIGNALING & BEHAVIOR 2024; 19:2326870. [PMID: 38465846 PMCID: PMC10936674 DOI: 10.1080/15592324.2024.2326870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 02/29/2024] [Indexed: 03/12/2024]
Abstract
One of the most destructive diseases affecting rice is rice blast, which is brought on by the rice blast fungus Magnaporthe oryzae. The preventive measures, however, are not well established. To effectively reduce the negative effects of rice blasts on crop yields, it is imperative to comprehend the dynamic interactions between pathogen resistance and patterns of host carbon allocation. This review explores the relationship between variations in carbon allocation and rice plants' ability to withstand the damaging effects of M. oryzae. The review highlights potential strategies for altering host carbon allocation including transgenic, selective breeding, crop rotation, and nutrient management practices as a promising avenue for enhancing rice blast resistance. This study advances our knowledge of the interaction between plants' carbon allocation and M. oryzae resistance and provides stakeholders and farmers with practical guidance on mitigating the adverse effects of the rice blast globally. This information may be used in the future to create varieties that are resistant to M. oryzae.
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Affiliation(s)
- Gideon Sadikiel Mmbando
- Department of Biology, College of Natural and Mathematical Sciences, University of Dodoma, Dodoma, Tanzania
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3
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Pan S, Zhang Z, Pang W. The causal relationship between bacterial pneumonia and diabetes: a two-sample mendelian randomization study. Islets 2024; 16:2291885. [PMID: 38095344 PMCID: PMC10730180 DOI: 10.1080/19382014.2023.2291885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/03/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Previous observational studies have established the high prevalence of bacterial pneumonia in diabetic patients, which in turn leads to increased mortality. However, the presence of a causal connection between bacterial pneumonia and diabetes remains unobserved. METHODS We chose genome-wide significant (Ρ < 1 × 10-5 and Ρ < 1 × 10-6) and independent (r2 < 0.001) single-nucleotide polymorphisms (SNPs) as instrumental variables (IVs) to proceed a bidirectional two-sample MR study. The extracted SNPs explored the relationship between bacterial pneumonia and diabetes by Inverse variance weighted (IVW), MR-Egger, and weighted median methods. In addition, we conducted the Heterogeneity test, the Pleiotropy test, MR-presso and the Leave-one-out (LOO) sensitivity test to validate the reliability of results. RESULTS In an MR study with bacterial pneumonia as an exposure factor, four different types of diabetes as outcome. It was observed that bacterial pneumonia increases the incidence of GDM (OR = 1.150 (1.027-1.274, P = 0.011) and T1DM (OR = 1.277 (1.024-1.531), P = 0.016). In the reverse MR analysis, it was observed that GDM (OR = 1.112 (1.023-1.201, P = 0.009) is associated with an elevated risk of bacterial pneumonia. However, no significant association was observed bacterial pneumonia with T1DM and other types of diabetes (P > 0.05). CONCLUSION This study utilizing MR methodology yields robust evidence supporting a bidirectional causal association between bacterial pneumonia and GDM. Furthermore, our findings suggest a plausible causal link between bacterial pneumonia and T1DM.
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Affiliation(s)
- Songying Pan
- The School of Public Health, Guilin Medical University, Guilin, Guangxi, China
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, Guilin Medical University, Guilin, Guangxi, China
| | - Zhongqi Zhang
- The School of Public Health, Guilin Medical University, Guilin, Guangxi, China
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, Guilin Medical University, Guilin, Guangxi, China
| | - Weiyi Pang
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, Guilin Medical University, Guilin, Guangxi, China
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Meepagala KM, Anderson CM, Techen N, Duke SO. Pantoea ananatis, a plant growth stimulating bacterium, and its metabolites isolated from Hydrocotyle umbellata (dollarweed). PLANT SIGNALING & BEHAVIOR 2024; 19:2331894. [PMID: 38516998 PMCID: PMC10962587 DOI: 10.1080/15592324.2024.2331894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/22/2024] [Indexed: 03/23/2024]
Abstract
A bacterium growing on infected leaves of Hydrocotyle umbellata, commonly known as dollarweed, was isolated and identified as Pantoea ananatis. An ethyl acetate extract of tryptic soy broth (TSB) liquid culture filtrate of the bacterium was subjected to silica gel chromatography to isolate bioactive molecules. Indole was isolated as the major compound that gave a distinct, foul odor to the extract, together with phenethyl alcohol, phenol, tryptophol, N-acyl-homoserine lactone, 3-(methylthio)-1-propanol, cyclo(L-pro-L-tyr), and cyclo(dehydroAla-L-Leu). This is the first report of the isolation of cyclo(dehydroAla-L-Leu) from a Pantoea species. Even though tryptophol is an intermediate in the indoleacetic acid (IAA) pathway, we were unable to detect or isolate IAA. We investigated the effect of P. ananatis inoculum on the growth of plants. Treatment of Lemna paucicostata Hegelm plants with 4 × 109 colony forming units of P. ananatis stimulated their growth by ca. five-fold after 13 days. After 13 days of treatment, some control plants were browning, but treated plants were greener and no plants were browning. The growth of both Cucumis sativus (cucumber) and Sorghum bicolor (sorghum) plants was increased by ca. 20 to 40%, depending on the growth parameter and species, when the rhizosphere was treated with the bacterium after germination at the same concentration. Plant growth promotion by Pantoea ananatis could be due to the provision of the IAA precursor indole.
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Affiliation(s)
- Kumudini M. Meepagala
- United States Department of Agriculture, Agricultural Research Service, Natural Products Utilization Research Unit, University, USA
| | - Caleb M. Anderson
- United States Department of Agriculture, Agricultural Research Service, Natural Products Utilization Research Unit, University, USA
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Natascha Techen
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, USA
| | - Stephen O. Duke
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, USA
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Huynh DT, Nolfi E, Medfai L, van Ulsen P, Jong WSP, Sijts AJAM, Luirink J. Intranasal delivery of Salmonella OMVs decorated with Chlamydia trachomatis antigens induces specific local and systemic immune responses. Hum Vaccin Immunother 2024; 20:2330768. [PMID: 38517203 PMCID: PMC10962599 DOI: 10.1080/21645515.2024.2330768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 03/12/2024] [Indexed: 03/23/2024] Open
Abstract
Chlamydia trachomatis is an obligate intracellular pathogen responsible for the most prevalent bacterial sexually transmitted disease globally. The high prevalence of chlamydial infections underscores the urgent need for licensed and effective vaccines to prevent transmission in populations. Bacterial outer membrane vesicles (OMVs) have emerged as promising mucosal vaccine carriers due to their inherent adjuvant properties and the ability to display heterologous antigens. In this proof-of-concept study, we evaluated the immunogenicity of Salmonella OMVs decorated with C. trachomatis MOMP-derived CTH522 or HtrA antigens in mice. Following a prime-boost intranasal vaccination approach, two OMV-based C. trachomatis vaccines elicited significant humoral responses specific to the antigens in both systemic and vaginal compartments. Furthermore, we demonstrated strong antigen-specific IFN-γ and IL17a responses in splenocytes and cervical lymph node cells of vaccinated mice, indicating CD4+ Th1 and Th17 biased immune responses. Notably, the OMV-CTH522 vaccine also induced the production of spleen-derived CD8+ T cells expressing IFN-γ. In conclusion, these results highlight the potential of OMV-based C. trachomatis vaccines for successful use in future challenge studies and demonstrate the suitability of our modular OMV platform for intranasal vaccine applications.
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Affiliation(s)
- Dung T. Huynh
- R&D department, Abera Bioscience AB, Uppsala, Sweden
- Group of Molecular Microbiology, Amsterdam Institute for Life and Environment (A-LIFE), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Emanuele Nolfi
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Lobna Medfai
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Peter van Ulsen
- Group of Molecular Microbiology, Amsterdam Institute for Life and Environment (A-LIFE), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | | | - Alice J. A. M. Sijts
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Joen Luirink
- R&D department, Abera Bioscience AB, Uppsala, Sweden
- Group of Molecular Microbiology, Amsterdam Institute for Life and Environment (A-LIFE), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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6
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Song Y, Lan Y, Li K, Qiao D, Cao Y, Xu H. Regulation of a novel DsGATA1 from Dunaliella salina on the synthesis of carotenoids under red light. Appl Microbiol Biotechnol 2024; 108:82. [PMID: 38189955 DOI: 10.1007/s00253-023-12894-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 10/31/2023] [Accepted: 11/22/2023] [Indexed: 01/09/2024]
Abstract
Dunaliella salina is a high-quality industrial effector for carotenoid production. The mechanism by which red light regulates carotenoid synthesis is still unclear. In this study, a transcription factor of DsGATA1 with a distinct structure was discovered in D. salina. The recognition motif of DsGATA1 was comparable to that of plant and fungal GATA, despite its evolutionary proximity to animal-derived GATA. The expression of DsGATA1 in D. salina was still noticeably decreased when exposed to red light. Analysis of physiological and biochemical transcriptomic data from overexpressed, interfering, and wild-type strains of DsGATA1 revealed that DsGATA1 acts as a global regulator of D. salina carotenoid synthesis. The upregulated genes in the CBP pathway by DsGATA1 were involved in its regulation of the synthesis of carotenoids. DsGATA1 also enhanced carotenoid accumulation under red light by affecting N metabolism. DsGATA1 was found to directly bind to the promoter of nitrate reductase to activate its expression, promoting D. salina nitrate uptake and accelerating biomass accumulation. DsGATA1 affected the expression of the genes encoding GOGAT, GDH, and ammonia transporter proteins. Moreover, our study revealed that the regulation of N metabolism by DsGATA1 led to the production of NO molecules that inhibited carotenoid synthesis. However, DsGATA1 significantly enhanced carotenoid synthesis by NO scavenger removal of NO. The D. salina carotenoid accumulation under red light was elevated by 46% in the presence of overexpression of DsGATA1 and NO scavenger. Nevertheless, our results indicated that DsGATA1 could be an important target for engineering carotenoid production. KEY POINTS: • DsGATA1 with a distinct structure and recognition motif was found in D. salina • DsGATA1 enhanced carotenoid production and biomass in D. salina under red light • DsGATA1 is involved in the regulation of N metabolism and carotenoid synthesis.
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Affiliation(s)
- Yao Song
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China
| | - Yanhong Lan
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China
| | - Ke Li
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China
| | - Dairong Qiao
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China
| | - Yi Cao
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China
| | - Hui Xu
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China.
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7
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Kacholi DS. A comprehensive review of antimalarial medicinal plants used by Tanzanians. PHARMACEUTICAL BIOLOGY 2024; 62:133-152. [PMID: 38270178 PMCID: PMC10812860 DOI: 10.1080/13880209.2024.2305453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 01/09/2024] [Indexed: 01/26/2024]
Abstract
CONTEXT Tanzania has rich medicinal plant (MP) resources, and most rural inhabitants rely on traditional healing practices for their primary healthcare needs. However, available research evidence on antimalarial MPs is highly fragmented in the country. OBJECTIVE This systematic review compiles ethnomedicinal research evidence on MPs used by Tanzanians as antimalarials. MATERIALS AND METHODS A systematic web search was conducted using various electronic databases and grey materials to gather relevant information on antimalarial MPs utilized by Tanzanians. The review was per the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. The data were collected from 25 articles, and MS Excel software was used to analyse relevant ethnobotanical information using descriptive statistics. RESULTS A total of 227 MPs belonging to 67 botanical families and 180 genera were identified. Fabaceae (15.9%) is the most frequently utilized family. The ethnobotanical recipes analysis indicated leaves (40%) and trees (44%) are the preferred MPs part and life form, respectively. Decoctions (67%) are the dominant preparation method of remedies. Of the recorded MPs, 25.9% have been scientifically investigated for antimalarial activities with positive results. However, 74.1% of MPs have no scientific records on antimalarial activities, but they could be potential sources of remedies. CONCLUSIONS The study discloses a wealth of antimalarial MPs possessed by Tanzanians and suggests a need for research to authenticate the healing potential of antimalarial compounds from the unstudied MPs. Additionally, it indicates that some of the presented MPs are potential sources for developing safe, effective and affordable antimalarial drugs.
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Affiliation(s)
- David Sylvester Kacholi
- Department of Biological Sciences, Dar es Salaam University College of Education (DUCE), University of Dar es Salaam (UDSM), Dar es Salaam, Tanzania
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8
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Xia W, Shi N, Li C, Tang A. RNA-Seq and miRNA-Seq data from Epstein-Barr virus-infected tree shrews reveal a ceRNA network contributing to immune microenvironment regulation. Virulence 2024; 15:2306795. [PMID: 38251668 PMCID: PMC10826628 DOI: 10.1080/21505594.2024.2306795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
Epstein-Barr virus (EBV) infection in humans is ubiquitous and associated with various diseases. Remodeling of the immune microenvironment is the primary cause of EBV infection and pathogenesis; however, the underlying mechanism has not been fully elucidated. In this study, we used whole-transcriptome RNA-Seq to detect mRNAs, long non-coding RNAs (lncRNA), and microRNA (miRNA) profiles in the control group, 3 days, and 28 days after EBV infection, based on the tree shrew model that we reported previously. First, we estimated the proportion of 22 cell types in each sample using CIBERSORT software and identified 18 high-confidence DElncRNAs related to immune microenvironment regulation after EBV infection. Functional enrichment analysis of these differentially expressed lncRNAs primarily focused on the autophagy, endocytosis, and ferroptosis signalling pathways. Moreover, EBV infection affects miRNA expression patterns, and many miRNAs are silenced. Finally, three competing endogenous RNA regulatory networks were built using lncRNAs that significantly correlated with immune cell types, miRNAs that responded to EBV infection, and potentially targeted the mRNA of the miRNAs. Among them, MRPL42-AS-5 might act as an hsa-miR-296-5p "sponge" and compete with target mRNAs, thus increasing mRNA expression level, which could induce immune cell infiltration through the cellular senescence signalling pathway against EBV infection. Overall, we conducted a complete transcriptomic analysis of EBV infection in vivo for the first time and provided a novel perspective for further investigation of EBV-host interactions.
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Affiliation(s)
- Wei Xia
- Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Ministry of Education, Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Nanning, Guangxi, China
| | - Nan Shi
- Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Ministry of Education, Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Nanning, Guangxi, China
| | - Chaoqian Li
- Department of Emergency, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Anzhou Tang
- Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Ministry of Education, Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Nanning, Guangxi, China
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9
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Doloman A, Besteman MS, Sanders MG, Sousa DZ. Methanogenic partner influences cell aggregation and signalling of Syntrophobacterium fumaroxidans. Appl Microbiol Biotechnol 2024; 108:127. [PMID: 38229305 DOI: 10.1007/s00253-023-12955-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/15/2023] [Accepted: 12/01/2023] [Indexed: 01/18/2024]
Abstract
For several decades, the formation of microbial self-aggregates, known as granules, has been extensively documented in the context of anaerobic digestion. However, current understanding of the underlying microbial-associated mechanisms responsible for this phenomenon remains limited. This study examined morphological and biochemical changes associated with cell aggregation in model co-cultures of the syntrophic propionate oxidizing bacterium Syntrophobacterium fumaroxidans and hydrogenotrophic methanogens, Methanospirillum hungatei or Methanobacterium formicicum. Formerly, we observed that when syntrophs grow for long periods with methanogens, cultures tend to form aggregates visible to the eye. In this study, we maintained syntrophic co-cultures of S. fumaroxidans with either M. hungatei or M. formicicum for a year in a fed-batch growth mode to stimulate aggregation. Millimeter-scale aggregates were observed in both co-cultures within the first 5 months of cultivation. In addition, we detected quorum sensing molecules, specifically N-acyl homoserine lactones, in co-culture supernatants preceding the formation of macro-aggregates (with diameter of more than 20 μm). Comparative transcriptomics revealed higher expression of genes related to signal transduction, polysaccharide secretion and metal transporters in the late-aggregation state co-cultures, compared to the initial ones. This is the first study to report in detail both biochemical and physiological changes associated with the aggregate formation in syntrophic methanogenic co-cultures. KEYPOINTS: • Syntrophic co-cultures formed mm-scale aggregates within 5 months of fed-batch cultivation. • N-acyl homoserine lactones were detected during the formation of aggregates. • Aggregated co-cultures exhibited upregulated expression of adhesins- and polysaccharide-associated genes.
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Affiliation(s)
- Anna Doloman
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708, WE, Wageningen, The Netherlands.
| | - Maaike S Besteman
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708, WE, Wageningen, The Netherlands
| | - Mark G Sanders
- Laboratory of Food Chemistry, Wageningen University, Bornse Weilanden 9, 6708, WG, Wageningen, The Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708, WE, Wageningen, The Netherlands
- Centre for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, Princetonlaan 6, 3584, CB, Utrecht, The Netherlands
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Chen T, Wang Y, Chi X, Xiong L, Lu P, Wang X, Chen Y, Luo Q, Shen P, Xiao Y. Genetic, virulence, and antimicrobial resistance characteristics associated with distinct morphotypes in ST11 carbapenem-resistant Klebsiella pneumoniae. Virulence 2024; 15:2349768. [PMID: 38736039 PMCID: PMC11093053 DOI: 10.1080/21505594.2024.2349768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 04/16/2024] [Indexed: 05/14/2024] Open
Abstract
ST11 is the most common lineage among carbapenem-resistant Klebsiella pneumoniae (CRKP) infections in Asia. Diverse morphotypes resulting from genetic mutations are associated with significant differences in microbial characteristics among K. pneumoniae isolates. Here, we investigated the genetic determinants and critical characteristics associated with distinct morphotypes of ST11 CRKP. An ST11-KL47 CRKP isolate carrying a pLVPK-like virulence plasmid was isolated from a patient with a bloodstream infection; the isolate had the "mcsw" morphotype. Two distinct morphotypes ("ntrd" and "msdw") were derived from this strain during in vitro passage. Whole genome sequencing was used to identify mutations that cause the distinct morphotypes of ST11 CRKP. Transmission electron microscopy, antimicrobial susceptibility tests, growth assays, biofilm formation, virulence assays, membrane permeability assays, and RNA-seq analysis were used to investigate the specific characteristics associated with different morphotypes of ST11 CRKP. Compared with the parental mcsw morphotype, the ntrd morphotype resulted from mutation of genes involved in capsular polysaccharide biosynthesis (wza, wzc, and wbaP), a result validated by gene knockout experiments. This morphotype showed capsule deficiency and lower virulence potential, but higher biofilm production. By contrast, the msdw morphotype displayed competition deficiency and increased susceptibility to chlorhexidine and polymyxin B. Further analyses indicated that these characteristics were caused by interruption of the sigma factor gene rpoN by insertion mutations and deletion of the rpoN gene, which attenuated membrane integrity presumably by downregulating the phage shock protein operon. These data expand current understanding of genetic, virulence, and antimicrobial resistance characteristics associated with distinct morphotypes in ST11 CRKP.
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Affiliation(s)
- Tao Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yuan Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiaohui Chi
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Luying Xiong
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ping Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xueting Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yunbo Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qixia Luo
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ping Shen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shandong, China
| | - Yonghong Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shandong, China
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11
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Burke Ó, Zeden MS, O'Gara JP. The pathogenicity and virulence of the opportunistic pathogen Staphylococcus epidermidis. Virulence 2024; 15:2359483. [PMID: 38868991 DOI: 10.1080/21505594.2024.2359483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 05/19/2024] [Indexed: 06/14/2024] Open
Abstract
The pervasive presence of Staphylococcus epidermidis and other coagulase-negative staphylococci on the skin and mucous membranes has long underpinned a casual disregard for the infection risk that these organisms pose to vulnerable patients in healthcare settings. Prior to the recognition of biofilm as an important virulence determinant in S. epidermidis, isolation of this microorganism in diagnostic specimens was often overlooked as clinically insignificant with potential delays in diagnosis and onset of appropriate treatment, contributing to the establishment of chronic infection and increased morbidity or mortality. While impressive progress has been made in our understanding of biofilm mechanisms in this important opportunistic pathogen, research into other virulence determinants has lagged S. aureus. In this review, the broader virulence potential of S. epidermidis including biofilm, toxins, proteases, immune evasion strategies and antibiotic resistance mechanisms is surveyed, together with current and future approaches for improved therapeutic interventions.
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Affiliation(s)
- Órla Burke
- Microbiology, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
| | | | - James P O'Gara
- Microbiology, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
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12
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Teng JLL, Tang Y, Wong SSY, Yeung ML, Cai JP, Chen C, Chan E, Fong JYH, Au-Yeung RKH, Xiong L, Lau TCK, Lau SKP, Woo PCY. Mycolyltransferase is important for biofilm formation and pathogenesis of Tsukamurella keratitis. Emerg Microbes Infect 2024; 13:2373317. [PMID: 38934251 PMCID: PMC11229725 DOI: 10.1080/22221751.2024.2373317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 06/22/2024] [Indexed: 06/28/2024]
Abstract
Tsukamurella, a group of multi-drug resistant, Gram-positive, aerobic, and partially acid-fast bacteria, are emerging causes of bacterial conjunctivitis and keratitis. However, the pathogenesis of Tsukamurella keratitis is largely unknown. To address this, we used New Zealand White rabbits to develop the first eye infection model and conducted in vitro tests to study the pathogenesis mechanisms of Tsukamurella. There is increasing evidence that biofilms play a significant role in ocular infections, leading us to hypothesize that biofilm formation is crucial for effective Tsukamurella infection. In order to look for potential candidate genes which are important in biofilm formation and Tsukamurella keratitis. We performed genome sequencing of two ocular isolates, T. pulmonis-PW1004 and T. tyrosinosolvens-PW899, to identify potential virulence factors. Through in vitro and in vivo studies, we characterized their biological roles in mediating Tsukamurella keratitis. Our findings confirmed that Tsukamurella is an ocular pathogen by fulfilling Koch's postulates, and using genome sequence data, we identified tmytC, encoding a mycolyltransferase, as a crucial gene in biofilm formation and causing Tsukamurella keratitis in the rabbit model. This is the first report demonstrating the novel role of mycolyltransferase in causing ocular infections. Overall, our findings contribute to a better understanding of Tsukamurella pathogenesis and provide a potential target for treatment. Specific inhibitors targeting TmytC could serve as an effective treatment option for Tsukamurella infections.
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Affiliation(s)
- Jade Lee-Lee Teng
- Faculty of Dentistry, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, People’s Republic of China
| | - Ying Tang
- Faculty of Dentistry, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, People’s Republic of China
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, People’s Republic of China
| | - Samson Sai-Yin Wong
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, People’s Republic of China
| | - Man Lung Yeung
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, People’s Republic of China
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, People’s Republic of China
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People’s Republic of China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, People’s Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, Hong Kong, People’s Republic of China
| | - Jian-Pao Cai
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, People’s Republic of China
| | - Chen Chen
- Beijing Ditan Hospital, Capital Medical University, Beijing Key Laboratory of Emerging infectious Diseases, Beijing, People’s Republic of China
| | - Elaine Chan
- Faculty of Dentistry, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, People’s Republic of China
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, People’s Republic of China
| | - Jordan Yik-Hei Fong
- Faculty of Dentistry, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, People’s Republic of China
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, People’s Republic of China
| | - Rex Kwok-Him Au-Yeung
- Department of Pathology, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, People’s Republic of China
| | - Lifeng Xiong
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, People’s Republic of China
| | - Terrence Chi-Kong Lau
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, People’s Republic of China
| | - Susanna Kar-Pui Lau
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, People’s Republic of China
| | - Patrick Chiu-Yat Woo
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, People’s Republic of China
- Doctoral Program in Translational Medicine and Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- The iEGG and Animal Biotechnology Research Center, National Chung Hsing University, Taichung, Taiwan
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13
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Bing J, Du H, Guo P, Hu T, Xiao M, Lu S, Nobile CJ, Chu H, Huang G. Candida auris-associated hospitalizations and outbreaks, China, 2018-2023. Emerg Microbes Infect 2024; 13:2302843. [PMID: 38238874 PMCID: PMC10802803 DOI: 10.1080/22221751.2024.2302843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/03/2024] [Indexed: 01/23/2024]
Abstract
The emerging human fungal pathogen Candida auris has become a serious threat to public health. This pathogen has spread to 10 provinces in China as of December 2023. Here we describe 312 C. auris-associated hospitalizations and 4 outbreaks in healthcare settings in China from 2018 to 2023. Three genetic clades of C. auris have been identified during this period. Molecular epidemiological analyses indicate that C. auris has been introduced and local transmission has occurred in multiple instances in China. Most C. auris isolated from China (98.7%) exhibited resistance to fluconazole, while only a small subset of strains were resistant to amphotericin B (4.2%) and caspofungin (2.2%).
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Affiliation(s)
- Jian Bing
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
- Department of Infectious Diseases, Huashan Hospital, Shanghai Institute of Infectious Disease and Biosecurity, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Han Du
- Department of Infectious Diseases, Huashan Hospital, Shanghai Institute of Infectious Disease and Biosecurity, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Penghao Guo
- Department of Clinical Laboratory, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Tianren Hu
- Department of Infectious Diseases, Huashan Hospital, Shanghai Institute of Infectious Disease and Biosecurity, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Meng Xiao
- Department of Laboratory Medicine, Sate Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
| | - Sha Lu
- Department of Dermatology and Venereology, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Clarissa J. Nobile
- Department of Molecular and Cell Biology, University of California, Merced, Merced, USA
- Health Sciences Research Institute, University of California, Merced, Merced, USA
| | - Haiqing Chu
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Guanghua Huang
- Department of Infectious Diseases, Huashan Hospital, Shanghai Institute of Infectious Disease and Biosecurity, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
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14
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He M, Yin S, Huang X, Li Y, Li B, Gong T, Liu Q. Insights into the regulatory role of bacterial sncRNA and its extracellular delivery via OMVs. Appl Microbiol Biotechnol 2024; 108:29. [PMID: 38159117 DOI: 10.1007/s00253-023-12855-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 10/11/2023] [Accepted: 10/20/2023] [Indexed: 01/03/2024]
Abstract
Small noncoding RNAs (sncRNAs) play important regulatory roles in bacterial physiological processes and host-pathogen interactions. Meanwhile, bacterial outer membrane vesicles (OMVs), as naturally secreted outer membrane structures, play a vital role in the interaction between bacteria and their living environment, including the host environment. However, most current studies focus on the biological functions of sncRNAs in bacteria or hosts, while neglecting the roles and regulatory mechanisms of the OMVs that encapsulate these sncRNAs. Therefore, this review aims to summarize the intracellular regulatory roles of bacterial sncRNAs in promoting pathogen survival by regulating virulence, modulating bacterial drug resistance, and regulating iron metabolism, and their extracellular regulatory function for influencing host immunity through host-pathogen interactions. Additionally, we introduce the key role played by OMVs, which serve as important cargoes in bacterial sncRNA-host interactions. We propose emerging pathways of sncRNA action to further discuss the mode of host-pathogen interactions, highlighting that the inhibition of sncRNA delivery by OMVs may prevent the occurrence of infection to some extent. Hence, this review lays the foundation for future prophylactic treatments against bacterial infections and strategies for addressing bacterial drug resistance. KEY POINTS: •sncRNAs have intracellular and extracellular regulatory functions in bacterial physiological processes and host-pathogen interactions. •OMVs are potential mediators between bacterial sncRNAs and host cells. •OMVs encapsulating sncRNAs have more potential biological functions.
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Affiliation(s)
- Mengdan He
- Center for Molecular Diagnosis and Precision Medicine, The Department of Clinical Laboratory, Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, China
- Department of Medical Microbiology, School of Medicine, Nanchang University, Nanchang, 330006, China
| | - Shuanshuan Yin
- Center for Molecular Diagnosis and Precision Medicine, The Department of Clinical Laboratory, Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, China
- Department of Medical Microbiology, School of Medicine, Nanchang University, Nanchang, 330006, China
| | - Xinlei Huang
- Gannan Medical University, Ganzhou, 341000, Jiangxi, China
| | - Yi Li
- Center for Molecular Diagnosis and Precision Medicine, The Department of Clinical Laboratory, Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, China
- Department of Medical Microbiology, School of Medicine, Nanchang University, Nanchang, 330006, China
| | - Biaoxian Li
- Center for Molecular Diagnosis and Precision Medicine, The Department of Clinical Laboratory, Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - Tian Gong
- Center for Molecular Diagnosis and Precision Medicine, The Department of Clinical Laboratory, Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, China.
| | - Qiong Liu
- Center for Molecular Diagnosis and Precision Medicine, The Department of Clinical Laboratory, Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, China.
- Department of Medical Microbiology, School of Medicine, Nanchang University, Nanchang, 330006, China.
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15
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Novak JK, Gardner JG. Current models in bacterial hemicellulase-encoding gene regulation. Appl Microbiol Biotechnol 2024; 108:39. [PMID: 38175245 PMCID: PMC10766802 DOI: 10.1007/s00253-023-12977-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024]
Abstract
The discovery and characterization of bacterial carbohydrate-active enzymes is a fundamental component of biotechnology innovation, particularly for renewable fuels and chemicals; however, these studies have increasingly transitioned to exploring the complex regulation required for recalcitrant polysaccharide utilization. This pivot is largely due to the current need to engineer and optimize enzymes for maximal degradation in industrial or biomedical applications. Given the structural simplicity of a single cellulose polymer, and the relatively few enzyme classes required for complete bioconversion, the regulation of cellulases in bacteria has been thoroughly discussed in the literature. However, the diversity of hemicelluloses found in plant biomass and the multitude of carbohydrate-active enzymes required for their deconstruction has resulted in a less comprehensive understanding of bacterial hemicellulase-encoding gene regulation. Here we review the mechanisms of this process and common themes found in the transcriptomic response during plant biomass utilization. By comparing regulatory systems from both Gram-negative and Gram-positive bacteria, as well as drawing parallels to cellulase regulation, our goals are to highlight the shared and distinct features of bacterial hemicellulase-encoding gene regulation and provide a set of guiding questions to improve our understanding of bacterial lignocellulose utilization. KEY POINTS: • Canonical regulatory mechanisms for bacterial hemicellulase-encoding gene expression include hybrid two-component systems (HTCS), extracytoplasmic function (ECF)-σ/anti-σ systems, and carbon catabolite repression (CCR). • Current transcriptomic approaches are increasingly being used to identify hemicellulase-encoding gene regulatory patterns coupled with computational predictions for transcriptional regulators. • Future work should emphasize genetic approaches to improve systems biology tools available for model bacterial systems and emerging microbes with biotechnology potential. Specifically, optimization of Gram-positive systems will require integration of degradative and fermentative capabilities, while optimization of Gram-negative systems will require bolstering the potency of lignocellulolytic capabilities.
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Affiliation(s)
- Jessica K Novak
- Department of Biological Sciences, University of Maryland - Baltimore County, Baltimore, MD, USA
| | - Jeffrey G Gardner
- Department of Biological Sciences, University of Maryland - Baltimore County, Baltimore, MD, USA.
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16
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Ren D, Xiong S, Ren Y, Yang X, Zhao X, Jin J, Xu M, Liang T, Guo L, Weng L. Advances in therapeutic cancer vaccines: Harnessing immune adjuvants for enhanced efficacy and future perspectives. Comput Struct Biotechnol J 2024; 23:1833-1843. [PMID: 38707540 PMCID: PMC11066472 DOI: 10.1016/j.csbj.2024.04.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/19/2024] [Accepted: 04/20/2024] [Indexed: 05/07/2024] Open
Abstract
Preventive cancer vaccines are highly effective in preventing viral infection-induced cancer, but advances in therapeutic cancer vaccines with a focus on eliminating cancer cells through immunotherapy are limited. To develop therapeutic cancer vaccines, the integration of optimal adjuvants is a potential strategy to enhance or complement existing therapeutic approaches. However, conventional adjuvants do not satisfy the criteria of clinical trials for therapeutic cancer vaccines. To improve the effects of adjuvants in therapeutic cancer vaccines, effective vaccination strategies must be formulated and novel adjuvants must be identified. This review offers an overview of the current advancements in therapeutic cancer vaccines and highlights in situ vaccination approaches that can be synergistically combined with other immunotherapies by harnessing the adjuvant effects. Additionally, the refinement of adjuvant systems using cutting-edge technologies and the elucidation of molecular mechanisms underlying immunogenic cell death to facilitate the development of innovative adjuvants have been discussed.
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Affiliation(s)
- Dekang Ren
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Shizheng Xiong
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Yujie Ren
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Xueni Yang
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Xinmiao Zhao
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Jiaming Jin
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Miaomiao Xu
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Tingming Liang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China
| | - Li Guo
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Lixing Weng
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China
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17
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Jeong GJ, Khan F, Tabassum N, Kim YM. Motility of Acinetobacter baumannii: regulatory systems and controlling strategies. Appl Microbiol Biotechnol 2024; 108:3. [PMID: 38159120 DOI: 10.1007/s00253-023-12975-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/08/2023] [Accepted: 11/13/2023] [Indexed: 01/03/2024]
Abstract
Acinetobacter baumannii is a Gram-negative opportunistic zoonotic pathogenic bacterium that causes nosocomial infections ranging from minor to life-threatening. The clinical importance of this zoonotic pathogen is rapidly increasing due to the development of multiple resistance mechanisms and the synthesis of numerous virulence factors. Although no flagellum-mediated motility exists, it may move through twitching or surface-associated motility. Twitching motility is a coordinated multicellular movement caused by the extension, attachment, and retraction of type IV pili, which are involved in surface adherence and biofilm formation. Surface-associated motility is a kind of movement that does not need appendages and is most likely driven by the release of extra polymeric molecules. This kind of motility is linked to the production of 1,3-diaminopropane, lipooligosaccharide formation, natural competence, and efflux pump proteins. Since A. baumannii's virulence qualities are directly tied to motility, it is possible that its motility may be used as a specialized preventative or therapeutic measure. The current review detailed the signaling mechanism and involvement of various proteins in controlling A. baumannii motility. As a result, we have thoroughly addressed the role of natural and synthetic compounds that impede A. baumannii motility, as well as the underlying action mechanisms. Understanding the regulatory mechanisms behind A. baumannii's motility features will aid in the development of therapeutic drugs to control its infection. KEY POINTS: • Acinetobacter baumannii exhibits multiple resistance mechanisms. • A. baumannii can move owing to twitching and surface-associated motility. • Natural and synthetic compounds can attenuate A. baumannii motility.
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Affiliation(s)
- Geum-Jae Jeong
- Department of Food Science and Technology, Pukyong National University, Busan, 48513, Republic of Korea
| | - Fazlurrahman Khan
- Institute of Fisheries Sciences, Pukyong National University, Busan, 48513, Republic of Korea.
- Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan, 48513, Republic of Korea.
- Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan, 48513, Republic of Korea.
| | - Nazia Tabassum
- Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan, 48513, Republic of Korea
- Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan, 48513, Republic of Korea
| | - Young-Mog Kim
- Department of Food Science and Technology, Pukyong National University, Busan, 48513, Republic of Korea.
- Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan, 48513, Republic of Korea.
- Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan, 48513, Republic of Korea.
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18
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Wang HM, Hu GR, Luo WY, Li FL. The horizontal gene transfer of perchlorate reduction genomic island in three bacteria from an ecological niche. Appl Microbiol Biotechnol 2024; 108:22. [PMID: 38159121 DOI: 10.1007/s00253-023-12827-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 09/25/2023] [Accepted: 11/01/2023] [Indexed: 01/03/2024]
Abstract
Three new strains of dissimilatory perchlorate-reducing bacteria (DPRB), QD19-16, QD1-5, and P3-1, were isolated from an active sludge. Phylogenetic trees based on 16S rRNA genes indicated that QD19-16, QD1-5, and P3-1 belonged to Brucella, Acidovorax, and Citrobacter, respectively, expanding the distribution of DPRB in the Proteobacteria. The three strains were gram-negative and facultative anaerobes with rod-shaped cells without flagella, which were 1.0-1.6 μm long and 0.5-0.6 μm wide. The three DPRB strains utilized similar broad spectrum of electron donors and acceptors and demonstrated a similar capability to reduce perchlorate within 6 days. The enzyme activity of perchlorate reductase in QD19-16 toward chlorate was higher than that toward perchlorate. The high sequence similarity of the perchlorate reductase operon and chlorite dismutase genes in the perchlorate reduction genomic islands (PRI) of the three strains implied that they were monophyletic origin from a common ancestral PRI. Two transposase genes (tnp1 and tnp2) were found in the PRIs of strain QD19-16 and QD1-5, but were absent in the strain P3-1 PRI. The presence of fragments of IR sequences in the P3-1 PRI suggested that P3-1 PRI had previously contained these two tnp genes. Therefore, it is plausible to suggest that a common ancestral PRI transferred across the strains Brucella sp. QD19-16, Acidovorax sp. QD1-5, and Citrobacter sp. P3-1 through horizontal gene transfer, facilitated by transposases. These results provided a direct evidence of horizontal gene transfer of PRI that could jump across phylogenetically unrelated bacteria through transposase. KEY POINTS: • Three new DPRB strains can effectively remove high concentration of perchlorate. • The PRIs of three DPRB strains are acquired from a single ancestral PRI. • PRIs are incorporated into different bacteria genome through HGT by transposase.
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Affiliation(s)
- Hao-Ming Wang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao C1 Refinery Engineering Research CenterQingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Guang-Rong Hu
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao C1 Refinery Engineering Research CenterQingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Wen-Yong Luo
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao C1 Refinery Engineering Research CenterQingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- School of Environmental and Municipal Engineering, Qingdao University of Technology, Qingdao, 266400, China
| | - Fu-Li Li
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao C1 Refinery Engineering Research CenterQingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
- Shandong Energy Institute, Qingdao, 266101, China.
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China.
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19
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Fang J, Zhou G, Zhao H, Xie D, Zhang J, Kües U, Xiao Y, Fang Z, Liu J. An apoptosis-inducing factor controls programmed cell death and laccase expression during fungal interactions. Appl Microbiol Biotechnol 2024; 108:135. [PMID: 38229306 DOI: 10.1007/s00253-023-12988-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/15/2023] [Accepted: 12/24/2023] [Indexed: 01/18/2024]
Abstract
Apoptotic-like programmed cell death (PCD) is one of the main strategies for fungi to resist environmental stresses and maintain homeostasis. The apoptosis-inducing factor (AIF) has been shown in different fungi to trigger PCD through upregulating reactive oxygen species (ROS). This study identified a mitochondrial localized AIF homolog, CcAIF1, from Coprinopsis cinerea monokaryon Okayama 7. Heterologous overexpression of CcAIF1 in Saccharomyces cerevisiae caused apoptotic-like PCD of the yeast cells. Ccaif1 was increased in transcription when C. cinerea interacted with Gongronella sp. w5, accompanied by typical apoptotic-like PCD in C. cinerea, including phosphatidylserine externalization and DNA fragmentation. Decreased mycelial ROS levels were observed in Ccaif1 silenced C. cinerea transformants during cocultivation, as well as reduction of the apoptotic levels, mycelial growth, and asexual sporulation. By comparison, Ccaif1 overexpression led to the opposite phenotypes. Moreover, the transcription and expression levels of laccase Lcc9 decreased by Ccaif1 silencing but increased firmly in Ccaif1 overexpression C. cinerea transformants in coculture. Thus, in conjunction with our previous report that intracellular ROS act as signal molecules to stimulate defense responses, we conclude that CcAIF1 is a regulator of ROS to promote apoptotic-like PCD and laccase expression in fungal-fungal interactions. In an axenic culture of C. cinerea, CcAIF1 overexpression and H2O2 stimulation together increased laccase secretion with multiplied production yield. The expression of two other normally silent isozymes, Lcc8 and Lcc13, was unexpectedly triggered along with Lcc9. KEY POINTS: • Mitochondrial CcAIF1 induces PCD during fungal-fungal interactions • CcAIF1 is a regulator of ROS to trigger the expression of Lcc9 for defense • CcAIF1 overexpression and H2O2 stimulation dramatically increase laccase production.
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Affiliation(s)
- Junnan Fang
- School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, 230601, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, 230601, Anhui, China
| | - Gang Zhou
- School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, 230601, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, 230601, Anhui, China
| | - Huifang Zhao
- School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, 230601, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, 230601, Anhui, China
| | - Dengdeng Xie
- School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, 230601, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, 230601, Anhui, China
| | - Jingna Zhang
- School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, 230601, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, 230601, Anhui, China
| | - Ursula Kües
- Molecular Wood Biotechnology and Technical Mycology, Büsgen‑Institute, University of Goettingen, Büsgenweg 2, 37077, Goettingen, Germany
| | - Yazhong Xiao
- School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, 230601, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, 230601, Anhui, China
| | - Zemin Fang
- School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China.
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, 230601, Anhui, China.
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, 230601, Anhui, China.
| | - Juanjuan Liu
- School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China.
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, 230601, Anhui, China.
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, 230601, Anhui, China.
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20
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Jian Y, Chen T, Yang Z, Xiang G, Xu K, Wang Y, Zhao N, He L, Liu Q, Li M. Small regulatory RNA RSaX28 promotes virulence by reinforcing the stability of RNAIII in community-associated ST398 clonotype Staphylococcus aureus. Emerg Microbes Infect 2024; 13:2341972. [PMID: 38597192 PMCID: PMC11034457 DOI: 10.1080/22221751.2024.2341972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 04/06/2024] [Indexed: 04/11/2024]
Abstract
Staphylococcus aureus (S. aureus) is a notorious pathogen that cause metastatic or complicated infections. Hypervirulent ST398 clonotype strains, remarkably increased in recent years, dominated Community-associated S. aureus (CA-SA) infections in the past decade in China. Small RNAs like RNAIII have been demonstrated to play important roles in regulating the virulence of S. aureus, however, the regulatory roles played by many of these sRNAs in the ST398 clonotype strains are still unclear. Through transcriptome screening and combined with knockout phenotype analysis, we have identified a highly transcribed sRNA, RSaX28, in the ST398 clonotype strains. Sequence analysis revealed that RSaX28 is highly conserved in the most epidemic clonotypes of S. aureus, but its high transcription level is particularly prominent in the ST398 clonotype strains. Characterization of RSaX28 through RACE and Northern blot revealed its length to be 533nt. RSaX28 is capable of promoting the hemolytic ability, reducing biofilm formation capacity, and enhancing virulence of S. aureus in the in vivo murine infection model. Through IntaRNA prediction and EMSA validation, we found that RSaX28 can specifically interact with RNAIII, promoting its stability and positively regulating the translation of downstream alpha-toxin while inhibiting the translation of Sbi, thereby regulating the virulence and biofilm formation capacity of the ST398 clonotype strains. RSaX28 is an important virulence regulatory factor in the ST398 clonotype S. aureus and represents a potential important target for future treatment and immune intervention against S. aureus infections.
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Affiliation(s)
- Ying Jian
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Tianchi Chen
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Ziyu Yang
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Guoxiu Xiang
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Kai Xu
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Yanan Wang
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Na Zhao
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Lei He
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Qian Liu
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Min Li
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
- Faculty of Medical Laboratory Science, College of Health Science and Technology, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
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21
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Seabaugh JA, Anderson DM. Pathogenicity and virulence of Yersinia. Virulence 2024; 15:2316439. [PMID: 38389313 PMCID: PMC10896167 DOI: 10.1080/21505594.2024.2316439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 02/04/2024] [Indexed: 02/24/2024] Open
Abstract
The genus Yersinia includes human, animal, insect, and plant pathogens as well as many symbionts and harmless bacteria. Within this genus are Yersinia enterocolitica and the Yersinia pseudotuberculosis complex, with four human pathogenic species that are highly related at the genomic level including the causative agent of plague, Yersinia pestis. Extensive laboratory, field work, and clinical research have been conducted to understand the underlying pathogenesis and zoonotic transmission of these pathogens. There are presently more than 500 whole genome sequences from which an evolutionary footprint can be developed that details shared and unique virulence properties. Whereas the virulence of Y. pestis now seems in apparent homoeostasis within its flea transmission cycle, substantial evolutionary changes that affect transmission and disease severity continue to ndergo apparent selective pressure within the other Yersiniae that cause intestinal diseases. In this review, we will summarize the present understanding of the virulence and pathogenesis of Yersinia, highlighting shared mechanisms of virulence and the differences that determine the infection niche and disease severity.
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Affiliation(s)
- Jarett A. Seabaugh
- Department of Veterinary Pathobiology, University of Missouri, Columbia, USA
| | - Deborah M. Anderson
- Department of Veterinary Pathobiology, University of Missouri, Columbia, USA
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22
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Lucidi M, Visaggio D, Migliaccio A, Capecchi G, Visca P, Imperi F, Zarrilli R. Pathogenicity and virulence of Acinetobacter baumannii: Factors contributing to the fitness in healthcare settings and the infected host. Virulence 2024; 15:2289769. [PMID: 38054753 PMCID: PMC10732645 DOI: 10.1080/21505594.2023.2289769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 11/27/2023] [Indexed: 12/07/2023] Open
Abstract
Acinetobacter baumannii is a common cause of healthcare-associated infections and hospital outbreaks, particularly in intensive care units. Much of the success of A. baumannii relies on its genomic plasticity, which allows rapid adaptation to adversity and stress. The capacity to acquire novel antibiotic resistance determinants and the tolerance to stresses encountered in the hospital environment promote A. baumannii spread among patients and long-term contamination of the healthcare setting. This review explores virulence factors and physiological traits contributing to A. baumannii infection and adaptation to the hospital environment. Several cell-associated and secreted virulence factors involved in A. baumannii biofilm formation, cell adhesion, invasion, and persistence in the host, as well as resistance to xeric stress imposed by the healthcare settings, are illustrated to give reasons for the success of A. baumannii as a hospital pathogen.
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Affiliation(s)
- Massimiliano Lucidi
- Department of Science, Roma Tre University, Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Daniela Visaggio
- Department of Science, Roma Tre University, Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
- Santa Lucia Foundation IRCCS, Rome, Italy
| | | | | | - Paolo Visca
- Department of Science, Roma Tre University, Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
- Santa Lucia Foundation IRCCS, Rome, Italy
| | - Francesco Imperi
- Department of Science, Roma Tre University, Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
- Santa Lucia Foundation IRCCS, Rome, Italy
| | - Raffaele Zarrilli
- Department of Public Health, University of Naples Federico II, Naples, Italy
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23
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Ji Y, Li J, Liang Y, Li L, Wang Y, Pi L, Xing P, Nomura CT, Chen S, Zhu C, Wang Q. Engineering the Tat-secretion pathway of Bacillus licheniformis for the secretion of cytoplasmic enzyme arginase. Appl Microbiol Biotechnol 2024; 108:89. [PMID: 38194145 DOI: 10.1007/s00253-023-12917-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/06/2023] [Accepted: 10/16/2023] [Indexed: 01/10/2024]
Abstract
The industrial bacterium Bacillus licheniformis has long been used as a microbial factory for the production of enzymes due to its ability to secrete copious amounts of native extracellular proteins and its generally regarded as safe (GRAS) status. However, most attempts to use B. licheniformis to produce heterologous and cytoplasmic enzymes primarily via the general secretory (Sec) pathway have had limited success. The twin-arginine transport (Tat) pathway offers a promising alternative for the extracellular export of Sec-incompatible proteins because it transports full, correctly folded proteins. However, compared to the Sec pathway, the yields of the Tat pathway have historically been too low for commercial use. To improve the export efficiency of the Tat pathway, we identified the optimal Tat-dependent signal peptides and increased the abundance of the Tat translocases, the signal peptidase (SPase), and the intracellular chaperones. These strategic modifications significantly improved the Tat-dependent secretion of the cytoplasmic enzyme arginase into the culture medium using B. licheniformis. The extracellular enzymatic activity of arginase showed a 5.2-fold increase after these modifications. Moreover, compared to the start strain B. licheniformis 0F3, the production of extracellular GFP was improved by 3.8 times using the strategic modified strain B. licheniformis 0F13, and the extracellular enzymatic activity of SOX had a 1.3-fold increase using the strain B. licheniformis 0F14. This Tat-based production chassis has the potential for enhanced production of Sec-incompatible enzymes, therefore expanding the capability of B. licheniformis as an efficient cellular factory for the production of high-value proteins. KEY POINTS: • Systematic genetic modification of Tat-pathway in B. licheniformis. • Significant enhancement of the secretion capacity of Tat pathway for delivery the cytoplasmic enzyme arginase. • A new platform for efficient extracellular production of Sec-incompatible enzymes.
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Affiliation(s)
- Yi Ji
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Science, Hubei University, Wuhan, 430062, People's Republic of China
| | - Junliang Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Science, Hubei University, Wuhan, 430062, People's Republic of China
| | - Yonglin Liang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Science, Hubei University, Wuhan, 430062, People's Republic of China
| | - Liang Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Science, Hubei University, Wuhan, 430062, People's Republic of China
| | - Yajun Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Science, Hubei University, Wuhan, 430062, People's Republic of China
| | - Li Pi
- Wuhan Grand Hoyo Co., Ltd, Wuhan, 430075, People's Republic of China
| | - Panpan Xing
- Wuhan Grand Hoyo Co., Ltd, Wuhan, 430075, People's Republic of China
| | - Christopher T Nomura
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive, Moscow, ID, 83844, USA
| | - Shouwen Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Science, Hubei University, Wuhan, 430062, People's Republic of China
| | - Chengjun Zhu
- Wuhan Grand Hoyo Co., Ltd, Wuhan, 430075, People's Republic of China.
| | - Qin Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Science, Hubei University, Wuhan, 430062, People's Republic of China.
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24
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Hasan M, He Z, Jia M, Leung ACF, Natarajan K, Xu W, Yap S, Zhou F, Chen S, Su H, Zhu K, Su H. Dynamic expedition of leading mutations in SARS-CoV-2 spike glycoproteins. Comput Struct Biotechnol J 2024; 23:2407-2417. [PMID: 38882678 PMCID: PMC11176665 DOI: 10.1016/j.csbj.2024.05.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 05/21/2024] [Accepted: 05/21/2024] [Indexed: 06/18/2024] Open
Abstract
The continuous evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which caused the recent pandemic, has generated countless new variants with varying fitness. Mutations of the spike glycoprotein play a particularly vital role in shaping its evolutionary trajectory, as they have the capability to alter its infectivity and antigenicity. We present a time-resolved statistical method, Dynamic Expedition of Leading Mutations (deLemus), to analyze the evolutionary dynamics of the SARS-CoV-2 spike glycoprotein. The proposed L -index of the deLemus method is effective in quantifying the mutation strength of each amino acid site and outlining evolutionarily significant sites, allowing the comprehensive characterization of the evolutionary mutation pattern of the spike glycoprotein.
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Affiliation(s)
- Muhammad Hasan
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Zhouyi He
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Mengqi Jia
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Alvin C F Leung
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | | | - Wentao Xu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Shanqi Yap
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Feng Zhou
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Shihong Chen
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Hailei Su
- Bengbu Hospital of Traditional Chinese Medicine, 4339 Huai-shang Road, Anhui 233080, China
| | - Kaicheng Zhu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Haibin Su
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
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25
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Wen L, Cui Y, Huang L, Wei C, Wang G, Zhang J, Jiang Y, Wei Y, Shen P. Changes of composition and antibiotic resistance of fecal coliform bacteria in municipal wastewater treatment plant. J Environ Sci (China) 2024; 146:241-250. [PMID: 38969452 DOI: 10.1016/j.jes.2023.09.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 09/07/2023] [Accepted: 09/10/2023] [Indexed: 07/07/2024]
Abstract
The dynamics of the composition and antibiotic resistance of the fecal coliform bacteria (FCB) in a typical wastewater treatment plant (WWTP) were investigated concerning the seasonal changes. Results showed that WWTP could remove the FCB concentration by 3∼5 logs within the effluent of 104∼105 CFU/L, but the antibiotic resistant rate of FCB species increased significantly after WWTP. The dominant FCB changed from Escherichia coli in the influent (∼73.0%) to Klebsiella pneumoniae in the effluent (∼53.3%) after WWTP, where the Escherichia coli was removed the most, while Klebsiella pneumoniae was the most persistent. The secondary tank removed the most of FCB (by 3∼4 logs) compared to other processes, but increased all the concerned antibiotic resistant rate. The potential super bugs of FCB community showing resistance to all the target antibiotics were selected in the biological treatment unit of WWTP. The FCB showed the highest multiple antibiotic resistance (92.9%) in total which even increased to 100% in the effluent. Klebsiella has the highest antibiotic resistant rate in FCB, with a multiple antibiotic resistance rate of 98.4%. These indicated that the Klebsiella pneumoniae not just Escherichia coli should be specially emphasized after WWTP concerning the health risk associated with FCB community.
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Affiliation(s)
- Luoyao Wen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Yunwei Cui
- College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Luodong Huang
- College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Chunzhong Wei
- Nanning Engineering & Technology Research Center for Water Safety, Guangxi Beitou Environmental Protection & Water Group Co., LTD., Nanning 530025, China
| | - Gangan Wang
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig 04318, Germany
| | - Junya Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig 04318, Germany; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yanbo Jiang
- Nanning Engineering & Technology Research Center for Water Safety, Guangxi Beitou Environmental Protection & Water Group Co., LTD., Nanning 530025, China; International Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China
| | - Yuansong Wei
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peihong Shen
- College of Life Science and Technology, Guangxi University, Nanning 530005, China.
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26
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Chiarelli DP, Sharma BD, Hon S, Bergamo LW, Lynd LR, Olson DG. Expression and characterization of monofunctional alcohol dehydrogenase enzymes in Clostridium thermocellum. Metab Eng Commun 2024; 19:e00243. [PMID: 39040142 PMCID: PMC11260334 DOI: 10.1016/j.mec.2024.e00243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 07/24/2024] Open
Abstract
Clostridium thermocellum is a thermophilic anaerobic bacterium that could be used for cellulosic biofuel production due to its strong native ability to consume cellulose, however its ethanol production ability needs to be improved to enable commercial application. In our previous strain engineering work, we observed a spontaneous mutation in the native adhE gene that reduced ethanol production. Here we attempted to complement this mutation by heterologous expression of 18 different alcohol dehydrogenase (adh) genes. We were able to express all of them successfully in C. thermocellum. Surprisingly, however, none of them increased ethanol production, and several actually decreased it. Our findings contribute to understanding the correlation between C. thermocellum ethanol production and Adh enzyme cofactor preferences. The identification of a set of adh genes that can be successfully expressed in this organism provides a foundation for future investigations into how the properties of Adh enzymes affect ethanol production.
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Affiliation(s)
- Daniela Prates Chiarelli
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
- Programa de Pós-Graduação Em Genética e Biologia Molecular, Instituto de Biologia (IB), Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Bishal Dev Sharma
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Shuen Hon
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Luana Walravens Bergamo
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
- Programa de Pós-Graduação Em Genética e Biologia Molecular, Instituto de Biologia (IB), Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Lee R. Lynd
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Daniel G. Olson
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
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27
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Miura D, Tsurigami R, Kato H, Wariishi H, Shimizu M. Pathway crosstalk between the central metabolic and heme biosynthetic pathways in Phanerochaete chrysosporium. Appl Microbiol Biotechnol 2024; 108:37. [PMID: 38183476 PMCID: PMC10771590 DOI: 10.1007/s00253-023-12846-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/28/2023] [Accepted: 10/03/2023] [Indexed: 01/08/2024]
Abstract
A comprehensive analysis to survey heme-binding proteins produced by the white-rot fungus Phanerochaete chrysosporium was achieved using a biotinylated heme-streptavidin beads system. Mitochondrial citrate synthase (PcCS), glyceraldehyde 3-phosphate dehydrogenase (PcGAPDH), and 2-Cys thioredoxin peroxidase (mammalian HBP23 homolog) were identified as putative heme-binding proteins. Among these, PcCS and PcGAPDH were further characterized using heterologously expressed recombinant proteins. Difference spectra of PcCS titrated with hemin exhibited an increase in the Soret absorbance at 414 nm, suggesting that the axial ligand of the heme is a His residue. The activity of PcCS was strongly inhibited by hemin with Ki oxaloacetate of 8.7 μM and Ki acetyl-CoA of 5.8 μM. Since the final step of heme biosynthesis occurred at the mitochondrial inner membrane, the inhibition of PcCS by heme is thought to be a physiological event. The inhibitory mode of the heme was similar to that of CoA analogues, suggesting that heme binds to PcCS at His347 at the AcCoA-CoA binding site, which was supported by the homology model of PcCS. PcGAPDH was also inhibited by heme, with a lower concentration than that for PcCS. This might be caused by the different location of these enzymes. From the integration of these phenomena, it was concluded that metabolic regulations by heme in the central metabolic and heme synthetic pathways occurred in the mitochondria and cytosol. This novel pathway crosstalk between the central metabolic and heme biosynthetic pathways, via a heme molecule, is important in regulating the metabolic balance (heme synthesis, ATP synthesis, flux balance of the tricarboxylic acid (TCA) cycle and cellular redox balance (NADPH production) during fungal aromatic degradation. KEY POINTS: • A comprehensive survey of heme-binding proteins in P. chrysosporium was achieved. • Several heme-binding proteins including CS and GAPDH were identified. • A novel metabolic regulation by heme in the central metabolic pathways was found.
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Affiliation(s)
- Daisuke Miura
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8566, Japan.
| | - Ryoga Tsurigami
- Faculty of Agriculture, Meijo University, Nagoya, Aichi, 468-8502, Japan
| | - Hiroyuki Kato
- Faculty of Agriculture, Meijo University, Nagoya, Aichi, 468-8502, Japan
| | - Hiroyuki Wariishi
- Faculty of Arts and Science, Kyushu University, Fukuoka, Fukuoka, 819-0395, Japan
| | - Motoyuki Shimizu
- Faculty of Agriculture, Meijo University, Nagoya, Aichi, 468-8502, Japan.
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28
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Larsen TG, Samaniego Castruita JA, Worning P, Westh H, Bartels MD. Within-host genomic evolution of methicillin-resistant Staphylococcus aureus in long-term carriers. Appl Microbiol Biotechnol 2024; 108:95. [PMID: 38212970 PMCID: PMC10784349 DOI: 10.1007/s00253-023-12932-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 11/14/2023] [Accepted: 11/27/2023] [Indexed: 01/13/2024]
Abstract
Assessing the genomic evolution of Staphylococcus aureus can help us understand how the bacteria adapt to its environment. In this study, we aimed to assess the mutation rate within 144 methicillin-resistant Staphylococcus aureus (MRSA) carriers with a carriage time from 4 to 11 years, including some carriers who belonged to the same households. We found that 23 of the 144 individuals had completely different MRSA types over time and were therefore not long-term carriers of the same MRSA. From the remaining 121 individuals, we performed whole-genome sequencing (WGS) on 424 isolates and then compared these pairwise using core genome multilocus sequence typing (cgMLST) and single-nucleotide polymorphism (SNP) analyses. We found a median within-host mutation rate in long-term MRSA carriers of 4.9 (3.4-6.9) SNPs/genome/year and 2.7 (1.8-4.2) allelic differences/genome/year, when excluding presumed recombination. Furthermore, we stratified the cohort into subgroups and found no significant difference between the median mutation rate of members of households, individuals with presumed continued exposure, e.g., from travel and persons without known continued exposure. Finally, we found that SNPs occurred at random within the genes in our cohort. KEY POINTS: • Median mutation rate within long-term MRSA carriers of 4.9 (3.4-6.9) SNPs/genome/year • Similar median mutation rates in subgroups (households, travelers) • No hotspots for SNPs within the genome.
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Affiliation(s)
- Tine Graakjær Larsen
- Department of Clinical Microbiology, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | | | - Peder Worning
- Department of Clinical Microbiology, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark
| | - Henrik Westh
- Department of Clinical Microbiology, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Mette Damkjær Bartels
- Department of Clinical Microbiology, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark.
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.
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Liu Y, Yuan J, Li Y, Bi Y, Prusky DB. The sensor protein AaSho1 regulates infection structures differentiation, osmotic stress tolerance and virulence via MAPK module AaSte11-AaPbs2-AaHog1 in Alternaria alternata. Comput Struct Biotechnol J 2024; 23:1594-1607. [PMID: 38680872 PMCID: PMC11047198 DOI: 10.1016/j.csbj.2024.04.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 04/01/2024] [Accepted: 04/11/2024] [Indexed: 05/01/2024] Open
Abstract
The high-osmolarity-sensitive protein Sho1 functions as a key membrane receptor in phytopathogenic fungi, which can sense and respond to external stimuli or stresses, and synergistically regulate diverse fungal biological processes through cellular signaling pathways. In this study, we investigated the biological functions of AaSho1 in Alternaria alternata, the causal agent of pear black spot. Targeted gene deletion revealed that AaSho1 is essential for infection structure differentiation, response to external stresses and synthesis of secondary metabolites. Compared to the wild-type (WT), the ∆AaSho1 mutant strain showed no significant difference in colony growth, morphology, conidial production and biomass accumulation. However, the mutant strain exhibited significantly reduced levels of melanin production, cellulase (CL) and ploygalacturonase (PG) activities, virulence, resistance to various exogenous stresses. Moreover, the appressorium and infection hyphae formation rates of the ∆AaSho1 mutant strain were significantly inhibited. RNA-Seq results showed that there were four branches including pheromone, cell wall stress, high osmolarity and starvation in the Mitogen-activated Protein Kinase (MAPK) cascade pathway. Furthermore, yeast two-hybrid experiments showed that AaSho1 activates the MAPK pathway via AaSte11-AaPbs2-AaHog1. These results suggest that AaSho1 of A. alternata is essential for fungal development, pathogenesis and osmotic stress response by activating the MAPK cascade pathway via Sho1-Ste11-Pbs2-Hog1.
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Affiliation(s)
- Yongxiang Liu
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, China
- College of Horticulture, Xinyang Agriculture and Forestry University, Xinyang, China
| | - Jing Yuan
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, China
| | - Yongcai Li
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, China
| | - Yang Bi
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, China
| | - Dov B. Prusky
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, China
- Institute of Postharvest and Food Sciences, Agricultural Research Organization Volcani Center Information Center, Rishon LeZion, Israel
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Yang X, Zeng J, Wang D, Zhou Q, Yu X, Wang Z, Bai T, Luan G, Xu Y. NagZ modulates the virulence of E. cloacae by acting through the gene of unknown function, ECL_03795. Virulence 2024; 15:2367652. [PMID: 38912723 PMCID: PMC11197897 DOI: 10.1080/21505594.2024.2367652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 06/09/2024] [Indexed: 06/25/2024] Open
Abstract
β-N-acetylglucosaminidase (NagZ), a cytosolic glucosaminidase, plays a pivotal role in peptidoglycan recycling. Previous research demonstrated that NagZ knockout significantly eradicated AmpC-dependent β-lactam resistance in Enterobacter cloacae. However, NagZ's role in the virulence of E. cloacae remains unclear. Our study, incorporating data on mouse and Galleria mellonella larval mortality rates, inflammation markers, and histopathological examinations, revealed a substantial reduction in the virulence of E. cloacae following NagZ knockout. Transcriptome sequencing uncovered differential gene expression between NagZ knockout and wild-type strains, particularly in nucleotide metabolism pathways. Further investigation demonstrated that NagZ deletion led to a significant increase in cyclic diguanosine monophosphate (c-di-GMP) levels. Additionally, transcriptome sequencing and RT-qPCR confirmed significant differences in the expression of ECL_03795, a gene with an unknown function but speculated to be involved in c-di-GMP metabolism due to its EAL domain known for phosphodiesterase activity. Interestingly, in ECL_03795 knockout strains, a notable reduction in the virulence was observed, and virulence was rescued upon complementation with ECL_03795. Consequently, our study suggests that NagZ's function on virulence is partially mediated through the ECL_03795→c-di-GMP pathway, providing insight into the development of novel therapies and strongly supporting the interest in creating highly efficient NagZ inhibitors.
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Affiliation(s)
- Xianggui Yang
- Department of Laboratory Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Jun Zeng
- Division of Pulmonary and Critical Care Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Dan Wang
- Department of Laboratory Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Qin Zhou
- Department of Laboratory Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Xuejing Yu
- Department of Internal Medicine, Division of Cardiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Zhenguo Wang
- Department of Stomatology, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Tingting Bai
- Department of Laboratory Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Guangxin Luan
- Department of Laboratory Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Ying Xu
- Department of Laboratory Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
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31
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Bai Y, Lei H, Song W, Shin SC, Wang J, Xiao B, Koçer ZA, Song MS, Webster R, Webby RJ, Wong SS, Zanin M. Amino acids in the polymerase complex of shorebird-isolated H1N1 influenza virus impact replication and host-virus interactions in mammalian models. Emerg Microbes Infect 2024; 13:2332652. [PMID: 38517705 PMCID: PMC11018082 DOI: 10.1080/22221751.2024.2332652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 03/15/2024] [Indexed: 03/24/2024]
Abstract
A diverse population of avian influenza A viruses (AIVs) are maintained in wild birds and ducks yet the zoonotic potential of AIVs in these environmental reservoirs and the host-virus interactions involved in mammalian infection are not well understood. In studies of a group of subtype H1N1 AIVs isolated from migratory wild birds during surveillance in North America, we previously identified eight amino acids in the polymerase genes PB2 and PB1 that were important for the transmissibility of these AIVs in a ferret model of human influenza virus transmission. In this current study we found that PB2 containing amino acids associated with transmissibility at 67, 152, 199, 508, and 649 and PB1 at 298, 642, and 667 were associated with more rapid viral replication kinetics, greater infectivity, more active polymerase complexes and greater kinetics of viral genome replication and transcription. Pathogenicity in the mouse model was also impacted, evident as greater weight loss and lung pathology associated with greater inflammatory lung cytokine expression. Further, these AIVs all contained the avian-type amino acids of PB2-E627, D701, G590, Q591 and T271. Therefore, our study provides novel insights into the role of the AIV polymerase complex in the zoonotic transmission of AIVs in mammals.
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Affiliation(s)
- Yaqin Bai
- HKU-Pasteur Research Pole, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China
- Guangzhou Medical University, Guangzhou, People’s Republic of China
- State Key Laboratory of Respiratory Diseases, Guangzhou, People’s Republic of China
| | - Hui Lei
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China
- Centre for Immunology & Infection, Hong Kong SAR, People's Republic of China
| | - Wenjun Song
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, People’s Republic of China
| | | | - Jiaqi Wang
- Guangzhou Medical University, Guangzhou, People’s Republic of China
- State Key Laboratory of Respiratory Diseases, Guangzhou, People’s Republic of China
| | - Biying Xiao
- Guangzhou Medical University, Guangzhou, People’s Republic of China
- State Key Laboratory of Respiratory Diseases, Guangzhou, People’s Republic of China
| | - Zeynep A. Koçer
- Emerging Viral Diseases Laboratory, Izmir Biomedicine and Genome Center, Izmir, Türkiye
- Department of Biomedicine and Health Technologies, Izmir International Biomedicine and Genome Institute, Izmir, Türkiye
| | - Min-Suk Song
- Department of Microbiology, Chungbuk National University Medical School, Chungbuk, Korea
| | - Robert Webster
- Department of Host-Microbe Interactions, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Richard J. Webby
- Department of Host-Microbe Interactions, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Sook-San Wong
- HKU-Pasteur Research Pole, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Mark Zanin
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People's Republic of China
- Centre for Immunology & Infection, Hong Kong SAR, People's Republic of China
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32
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Xi Y, Li X, Liu L, Xiu F, Yi X, Chen H, You X. Sneaky tactics: Ingenious immune evasion mechanisms of Bartonella. Virulence 2024; 15:2322961. [PMID: 38443331 PMCID: PMC10936683 DOI: 10.1080/21505594.2024.2322961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/20/2024] [Indexed: 03/07/2024] Open
Abstract
Gram-negative Bartonella species are facultative intracellular bacteria that can survive in the harsh intracellular milieu of host cells. They have evolved strategies to evade detection and degradation by the host immune system, which ensures their proliferation in the host. Following infection, Bartonella alters the initial immunogenic surface-exposed proteins to evade immune recognition via antigen or phase variation. The diverse lipopolysaccharide structures of certain Bartonella species allow them to escape recognition by the host pattern recognition receptors. Additionally, the survival of mature erythrocytes and their resistance to lysosomal fusion further complicate the immune clearance of this species. Certain Bartonella species also evade immune attacks by producing biofilms and anti-inflammatory cytokines and decreasing endothelial cell apoptosis. Overall, these factors create a challenging landscape for the host immune system to rapidly and effectively eradicate the Bartonella species, thereby facilitating the persistence of Bartonella infections and creating a substantial obstacle for therapeutic interventions. This review focuses on the effects of three human-specific Bartonella species, particularly their mechanisms of host invasion and immune escape, to gain new perspectives in the development of effective diagnostic tools, prophylactic measures, and treatment options for Bartonella infections.
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Affiliation(s)
- Yixuan Xi
- Institute of Pathogenic Biology, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical College, University of South China, Hengyang, China
| | - Xinru Li
- Institute of Pathogenic Biology, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical College, University of South China, Hengyang, China
| | - Lu Liu
- Institute of Pathogenic Biology, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical College, University of South China, Hengyang, China
| | - Feichen Xiu
- Institute of Pathogenic Biology, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical College, University of South China, Hengyang, China
| | - Xinchao Yi
- Institute of Pathogenic Biology, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical College, University of South China, Hengyang, China
| | - Hongliang Chen
- Chenzhou NO.1 People’s Hospital, The Affiliated Chenzhou Hospital, Hengyang Medical College, University of South China, ChenZhou, China
| | - Xiaoxing You
- Institute of Pathogenic Biology, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical College, University of South China, Hengyang, China
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33
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Qiu C, Liu Z. Positive selection and functional diversification of transcription factor Cmr1 homologs in Alternaria. Appl Microbiol Biotechnol 2024; 108:133. [PMID: 38229332 DOI: 10.1007/s00253-023-12893-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 12/04/2023] [Accepted: 12/07/2023] [Indexed: 01/18/2024]
Abstract
Transcription factor Cmr1 (Colletotrichum melanin regulation 1) and its homologs in several plant fungal pathogens are the regulators of the 1,8-dihydroxynaphthalene (DHN)-melanin biosynthesis pathway and have evolved functional diversification in morphology and pathogenicity. The fungal genus Alternaria comprises the group of "black fungi" that are rich in DHN-melanin in the primary cell wall and septa of the conidia. Some Alternaria species cause many economically important plant diseases worldwide. However, the evolution and function of Cmr1 homologs in Alternaria remain poorly understood. Here, we identified a total of forty-two Cmr1 homologs from forty-two Alternaria spp. and all contained one additional diverse fungal specific transcription factor motif. Phylogenetic analysis indicated the division of these homologs into five major clades and three branches. Dated phylogeny showed the A and D clades diverged latest and earliest, respectively. Molecular evolutionary analyses revealed that three amino acid sites of Cmr1 homologs in Alternaria were the targets of positive selection. Asmr1, the homolog of Cmr1 in the potato early blight pathogen, Alternaria solani was amplified and displayed the sequence conservation at the amino acid level in different A. solani isolates. Asmr1 was further confirmed to have the transcriptional activation activity and was upregulated during the early stage of potato infection. Deletion of asmr1 led to the decreased melanin content and pathogenicity, deformed conidial morphology, and responses to cell wall and fungicide stresses in A. solani. These results suggest positive selection and functional divergence have played a role in the evolution of Cmr1 homologs in Alternaria. KEY POINTS: • Cmr1 homologs were under positive selection in Alternaria species • Asmr1 is a functional transcription factor, involved in spore development, melanin biosynthesis, pathogenicity, and responses to cell wall and fungicide stresses in A. solani • Cmr1 might be used as a potential taxonomic marker of the genus Alternaria.
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Affiliation(s)
- Chaodong Qiu
- Department of Plant Pathology, School of Plant Protection, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Zhenyu Liu
- Department of Plant Pathology, School of Plant Protection, Anhui Agricultural University, Hefei, Anhui, 230036, China.
- Anhui Province Key Laboratory of Integrated Pest Management On Crops, Hefei, Anhui, 230036, China.
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Wen S, Zhao Y, Qi X, Cai M, Huang K, Liu H, Kong DX. Conformational plasticity of SpyCas9 induced by AcrIIA4 and AcrIIA2: Insights from molecular dynamics simulation. Comput Struct Biotechnol J 2024; 23:537-548. [PMID: 38235361 PMCID: PMC10791570 DOI: 10.1016/j.csbj.2023.12.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 12/06/2023] [Accepted: 12/22/2023] [Indexed: 01/19/2024] Open
Abstract
CRISPR-Cas9 systems constitute bacterial adaptive immune systems that protect against phage infections. Bacteriophages encode anti-CRISPR proteins (Acrs) that mitigate the bacterial immune response. However, the structural basis for their inhibitory actions from a molecular perspective remains elusive. In this study, through microsecond atomistic molecular dynamics simulations, we demonstrated the remarkable flexibility of Streptococcus pyogenes Cas9 (SpyCas9) and its conformational adaptability during interactions with AcrIIA4 and AcrIIA2. Specifically, we demonstrated that the binding of AcrIIA4 and AcrIIA2 to SpyCas9 induces a conformational rearrangement that causes spatial separation between the nuclease and cleavage sites, thus making the endonuclease inactive. This separation disrupts the transmission of signals between the protospacer adjacent motif recognition and nuclease domains, thereby impeding the efficient processing of double-stranded DNA. The simulation also reveals that AcrIIA4 and AcrIIA2 cause different structural variations of SpyCas9. Our research illuminates the precise mechanisms underlying the suppression of SpyCas9 by AcrIIA4 and AcrIIA2, thus presenting new possibilities for controlling genome editing with higher accuracy.
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Affiliation(s)
- Shuixiu Wen
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
| | - Yuxin Zhao
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
| | - Xinyu Qi
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
| | - Mingzhu Cai
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
| | - Kaisheng Huang
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
| | - Hui Liu
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
| | - De-Xin Kong
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
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35
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Su HL, Lai SJ, Tsai KC, Fung KM, Lung TL, Hsu HM, Wu YC, Liu CH, Lai HX, Lin JH, Tseng TS. Structure-guided identification and characterization of potent inhibitors targeting PhoP and MtrA to combat mycobacteria. Comput Struct Biotechnol J 2024; 23:1477-1488. [PMID: 38623562 PMCID: PMC11016868 DOI: 10.1016/j.csbj.2024.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 04/01/2024] [Accepted: 04/01/2024] [Indexed: 04/17/2024] Open
Abstract
Mycobacteria are causative agents of tuberculosis (TB), which is a global health concern. Drug-resistant TB strains are rapidly emerging, thereby necessitating the urgent development of new drugs. Two-component signal transduction systems (TCSs) are signaling pathways involved in the regulation of various bacterial behaviors and responses to environmental stimuli. Applying specific inhibitors of TCSs can disrupt bacterial signaling, growth, and virulence, and can help combat drug-resistant TB. We conducted a comprehensive pharmacophore-based inhibitor screening and biochemical and biophysical examinations to identify, characterize, and validate potential inhibitors targeting the response regulators PhoP and MtrA of mycobacteria. The constructed pharmacophore model Phar-PR-n4 identified effective inhibitors of formation of the PhoP-DNA complex: ST132 (IC50 = 29 ± 1.6 µM) and ST166 (IC50 = 18 ± 1.3 µM). ST166 (KD = 18.4 ± 4.3 μM) and ST132 (KD = 14.5 ± 0.1 μM) strongly targeted PhoP in a slow-on, slow-off manner. The inhibitory potency and binding affinity of ST166 and ST132 for MtrAC were comparable to those of PhoP. Structural analyses and molecular dynamics simulations revealed that ST166 and ST132 mainly interact with the α8-helix and C-terminal β-hairpin of PhoP, with functionally essential residue hotspots for structure-based inhibitor optimization. Moreover, ST166 has in vitro antibacterial activity against Macrobacterium marinum. Thus, ST166, with its characteristic 1,2,5,6-tetrathiocane and terminal sulphonic groups, has excellent potential as a candidate for the development of novel antimicrobial agents to combat pathogenic mycobacteria.
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Affiliation(s)
- Han-Li Su
- Department of Emergency Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi City 600, Taiwan
| | - Shu-Jung Lai
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung, Taiwan
| | - Keng-Chang Tsai
- National Research Institute of Chinese Medicine, Ministry of Health and Welfare, Taipei, Taiwan
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Kit-Man Fung
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei 11529, Taiwan
| | - Tse-Lin Lung
- Institute of Molecular Biology, National Chung Hsing University, Taichung,Taiwan
| | - Hsing-Mien Hsu
- Institute of Molecular Biology, National Chung Hsing University, Taichung,Taiwan
| | - Yi-Chen Wu
- Institute of Molecular Biology, National Chung Hsing University, Taichung,Taiwan
| | - Ching-Hui Liu
- Institute of Molecular Biology, National Chung Hsing University, Taichung,Taiwan
| | - Hui-Xiang Lai
- Institute of Molecular Biology, National Chung Hsing University, Taichung,Taiwan
| | - Jiun-Han Lin
- Department of Industrial Technology, Ministry of Economic Affairs, Taipei, Taiwan
- Food Industry Research and Development Institute, Hsinchu City, Taiwan
| | - Tien-Sheng Tseng
- Institute of Molecular Biology, National Chung Hsing University, Taichung,Taiwan
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Ding X, Zheng Z, Zhao G, Wang L, Wang H, Wang P. Adaptive laboratory evolution for improved tolerance of vitamin K in Bacillus subtilis. Appl Microbiol Biotechnol 2024; 108:75. [PMID: 38194140 DOI: 10.1007/s00253-023-12877-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 10/10/2023] [Accepted: 10/30/2023] [Indexed: 01/10/2024]
Abstract
Menaquinone-7 (MK-7), a subtype of vitamin K2 (VK2), assumes crucial roles in coagulation function, calcium homeostasis, and respiratory chain transmission. The production of MK-7 via microbial fermentation boasts mild technological conditions and high biocompatibility. Nevertheless, the redox activity of MK-7 imposes constraints on its excessive accumulation in microorganisms. To address this predicament, an adaptive laboratory evolution (ALE) protocol was implemented in Bacillus subtilis BS011, utilizing vitamin K3 (VK3) as a structural analog of MK-7. The resulting strain, BS012, exhibited heightened tolerance to high VK3 concentrations and demonstrated substantial enhancements in biofilm formation and total antioxidant capacity (T-AOC) when compared to BS011. Furthermore, MK-7 production in BS012 exceeded that of BS011 by 76% and 22% under static and shaking cultivation conditions, respectively. The molecular basis underlying the superior performance of BS012 was elucidated through genome and transcriptome analyses, encompassing observations of alterations in cell morphology, variations in central carbon and nitrogen metabolism, spore formation, and antioxidant systems. In summation, ALE technology can notably enhance the tolerance of B. subtilis to VK and increase MK-7 production, thus offering a theoretical framework for the microbial fermentation production of other VK2 subtypes. Additionally, the evolved strain BS012 can be developed for integration into probiotic formulations within the food industry to maintain intestinal flora homeostasis, mitigate osteoporosis risk, and reduce the incidence of cardiovascular disease. KEY POINTS: • Bacillus subtilis was evolved for improved vitamin K tolerance and menaquinone-7 (MK-7) production • Evolved strains formed wrinkled biofilms and elongated almost twofold in length • Evolved strains induced sporulation to improve tolerance when carbon was limited.
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Affiliation(s)
- Xiumin Ding
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
- Department of Health Inspection and Quarantine, Wannan Medical College, Wuhu, China
- University of Science and Technology of China, Hefei, China
| | - Zhiming Zheng
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China.
| | - Genhai Zhao
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Li Wang
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Han Wang
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Peng Wang
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China.
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37
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Dai Y, Liu R, Yue Y, Song N, Jia H, Ma Z, Gao X, Zhang M, Yuan X, Liu Q, Liu X, Li B, Wang W. A c-di-GMP binding effector STM0435 modulates flagellar motility and pathogenicity in Salmonella. Virulence 2024; 15:2331265. [PMID: 38532247 PMCID: PMC10978029 DOI: 10.1080/21505594.2024.2331265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 03/06/2024] [Indexed: 03/28/2024] Open
Abstract
Flagella play a crucial role in the invasion process of Salmonella and function as a significant antigen that triggers host pyroptosis. Regulation of flagellar biogenesis is essential for both pathogenicity and immune escape of Salmonella. We identified the conserved and unknown function protein STM0435 as a new flagellar regulator. The ∆stm0435 strain exhibited higher pathogenicity in both cellular and animal infection experiments than the wild-type Salmonella. Proteomic and transcriptomic analyses demonstrated dramatic increases in almost all flagellar genes in the ∆stm0435 strain compared to wild-type Salmonella. In a surface plasmon resonance assay, purified STM0435 protein-bound c-di-GMP had an affinity of ~8.383 µM. The crystal structures of apo-STM0435 and STM0435&c-di-GMP complex were determined. Structural analysis revealed that R33, R137, and D138 of STM0435 were essential for c-di-GMP binding. A Salmonella with STM1987 (GGDEF protein) or STM4264 (EAL protein) overexpression exhibits completely different motility behaviours, indicating that the binding of c-di-GMP to STM0435 promotes its inhibitory effect on Salmonella flagellar biogenesis.
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Affiliation(s)
- Yuanji Dai
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Ruirui Liu
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Yingying Yue
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Nannan Song
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Haihong Jia
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Zhongrui Ma
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Xueyan Gao
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Min Zhang
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Xilu Yuan
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Qing Liu
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Xiaoyu Liu
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Bingqing Li
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
- Key Lab for Biotech-Drugs of National Health Commission, Shandong First Medical University, Jinan, Shandong, China
- Key Lab for Rare & Uncommon Diseases of Shandong Province, Jinan, Shandong, China
| | - Weiwei Wang
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
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Li R, Zhu X, Zhang P, Wu X, Jin Q, Pan J. Ser/Thr protein kinase Stk1 phosphorylates the key transcriptional regulator AlgR to modulate virulence and resistance in Pseudomonas aeruginosa. Virulence 2024; 15:2367649. [PMID: 38898809 PMCID: PMC11197903 DOI: 10.1080/21505594.2024.2367649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 06/09/2024] [Indexed: 06/21/2024] Open
Abstract
Pseudomonas aeruginosa is one of the leading causes of nosocomial infections worldwide and has emerged as a serious public health threat, due in large part to its multiple virulence factors and remarkable resistance capabilities. Stk1, a eukaryotic-type Ser/Thr protein kinase, has been shown in our previous work to be involved in the regulation of several signalling pathways and biological processes. Here, we demonstrate that deletion of stk1 leads to alterations in several virulence- and resistance-related physiological functions, including reduced pyocyanin and pyoverdine production, attenuated twitching motility, and enhanced biofilm production, extracellular polysaccharide secretion, and antibiotic resistance. Moreover, we identified AlgR, an important transcriptional regulator, as a substrate for Stk1, with its phosphorylation at the Ser143 site catalysed by Stk1. Intriguingly, both the deletion of stk1 and the mutation of Ser143 of AlgR to Ala result in similar changes in the above-mentioned physiological functions. Furthermore, assays of algR expression in these strains suggest that changes in the phosphorylation state of AlgR, rather than its expression level, underlie changes in these physiological functions. These findings uncover Stk1-mediated phosphorylation of AlgR as an important mechanism for regulating virulence and resistance in P. aeruginosa.
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Affiliation(s)
- Rui Li
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Xuan Zhu
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Pengfei Zhang
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Xuan Wu
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Qian Jin
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Jianyi Pan
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
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Nakonieczna A, Topolska-Woś A, Łobocka M. New bacteriophage-derived lysins, LysJ and LysF, with the potential to control Bacillus anthracis. Appl Microbiol Biotechnol 2024; 108:76. [PMID: 38194144 PMCID: PMC10776502 DOI: 10.1007/s00253-023-12839-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 11/13/2023] [Accepted: 11/21/2023] [Indexed: 01/10/2024]
Abstract
Bacillus anthracis is an etiological agent of anthrax, a severe zoonotic disease that can be transmitted to people and cause high mortalities. Bacteriophages and their lytic enzymes, endolysins, have potential therapeutic value in treating infections caused by this bacterium as alternatives or complements to antibiotic therapy. They can also be used to identify and detect B. anthracis. Endolysins of two B. anthracis Wbetavirus phages, J5a and F16Ba which were described by us recently, differ significantly from the best-known B. anthracis phage endolysin PlyG from Wbetavirus genus bacteriophage Gamma and a few other Wbetavirus genus phages. They are larger than PlyG (351 vs. 233 amino acid residues), contain a signal peptide at their N-termini, and, by prediction, have a different fold of cell binding domain suggesting different structural basis of cell epitope recognition. We purified in a soluble form the modified versions of these endolysins, designated by us LysJ and LysF, respectively, and depleted of signal peptides. Both modified endolysins could lyse the B. anthracis cell wall in zymogram assays. Their activity against the living cells of B. anthracis and other species of Bacillus genus was tested by spotting on the layers of bacteria in soft agar and by assessing the reduction of optical density of bacterial suspensions. Both methods proved the effectiveness of LysJ and LysF in killing the anthrax bacilli, although the results obtained by each method differed. Additionally, the lytic efficiency of both proteins was different, which apparently correlates with differences in their amino acid sequence. KEY POINTS: • LysJ and LysF are B. anthracis-targeting lysins differing from lysins studied so far • LysJ and LysF could be overproduced in E. coli in soluble and active forms • LysJ and LysF are active in killing cells of B. anthracis virulent strains.
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Affiliation(s)
- Aleksandra Nakonieczna
- Military Institute of Hygiene and Epidemiology, Biological Threats Identification and Countermeasure Center, 24-100, Puławy, Poland.
| | | | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, 02-106, Warsaw, Poland
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40
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Wang K, Li W, Cui H, Qin S. Phylogenetic distribution and characterization of conserved C-di-GMP metabolizing proteins in filamentous cyanobacterium Arthrospira. Gene 2024; 927:148643. [PMID: 38844269 DOI: 10.1016/j.gene.2024.148643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/18/2024] [Accepted: 06/03/2024] [Indexed: 06/10/2024]
Abstract
Cyclic diguanosine monophosphate (c-di-GMP) is a second messenger in bacteria that regulates multiple biological functions, including biofilm formation, virulence, and intercellular communication. However, c-di-GMP signaling is virtually unknown in economically important filamentous cyanobacteria, Arthrospira. In this study, we predicted 31 genes encoding GGDEF-domain proteins from A. platensis NIES39 as potential diguanylate cyclases (DGCs). Phylogenetic distribution analysis showed five genes (RS09460, RS04865, RS26155, M01840, and E02220) with highly conserved distribution across 25 Arthrospira strains. Adc1 encoded by RS09460 was further characterized as a typical DGC. By establishing the genetic transformation system of Arthrospira, we demonstrated that the overexpression of Adc1 promoted the production of extracellular polymeric substances (EPS), which in turn caused the aggregation of filaments. We also confirmed that RS04865 and RS26155 may encode active DGCs, while enzymatic activity assays showed that proteins encoded by M01840 and E02220 have phosphodiesterase (PDE) activity. Meta-analysis revealed that the expression profiles of RS09460 and RS04865 were unaffected under 31 conditions, suggesting that they may function as conserved genes in maintaining the basal level of c-di-GMP in Arthrospira. In summary, this report will provide the basis for further studies of c-di-GMP signal in Arthrospira.
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Affiliation(s)
- Kang Wang
- Key Laboratory of Coastal Biology and Biological Resource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Wenjun Li
- Key Laboratory of Coastal Biology and Biological Resource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Hongli Cui
- Key Laboratory of Coastal Biology and Biological Resource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Song Qin
- Key Laboratory of Coastal Biology and Biological Resource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China.
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41
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Hu L, Li X, Li C, Wang L, Han L, Ni W, Zhou P, Hu S. Characterization of a novel multifunctional glycoside hydrolase family in the metagenome-assembled genomes of horse gut. Gene 2024; 927:148758. [PMID: 38977109 DOI: 10.1016/j.gene.2024.148758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 05/29/2024] [Accepted: 07/05/2024] [Indexed: 07/10/2024]
Abstract
The gut microbiota is a treasure trove of carbohydrate-active enzymes (CAZymes). To explore novel and efficient CAZymes, we analyzed the 4,142 metagenome-assembled genomes (MAGs) of the horse gut microbiota and found the MAG117.bin13 genome (Bacteroides fragilis) contains the highest number of polysaccharide utilisation loci sites (PULs), indicating its high capability for carbohydrate degradation. Bioinformatics analysis indicate that the PULs region of the MAG117.bin13 genome encodes many hypothetical proteins, which are important sources for exploring novel CAZymes. Interestingly, we discovered a hypothetical protein (595 amino acids). This protein exhibits potential CAZymes activity and has a lower similarity to CAZymes, we named it BfLac2275. We purified the protein using prokaryotic expression technology and studied its enzymatic function. The hydrolysis experiment of the polysaccharide substrate showed that the BfLac2275 protein has the ability to degrade α-lactose (156.94 U/mg), maltose (92.59 U/mg), raffinose (86.81 U/mg), and hyaluronic acid (5.71 U/mg). The enzyme activity is optimal at pH 5.0 and 30 ℃, indicating that the hypothetical protein BfLac2275 is a novel and multifunctional CAZymes in the glycoside hydrolases (GHs). These properties indicate that BfLac2275 has broad application prospects in many fields such as plant polysaccharide decomposition, food industry, animal feed additives and enzyme preparations. This study not only serves as a reference for exploring novel CAZymes encoded by gut microbiota but also provides an example for further studying the functional annotation of hypothetical genes in metagenomic assembly genomes.
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Affiliation(s)
- Lingling Hu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Xiaoyue Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Cunyuan Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Limin Wang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Xinjiang 832003, China
| | - Lin Han
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Wei Ni
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China.
| | - Ping Zhou
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Xinjiang 832003, China.
| | - Shengwei Hu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China.
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42
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Matenda RT, Rip D, Fernández Pierna JA, Baeten V, Williams PJ. Differentiation of Listeria monocytogenes serotypes using near infrared hyperspectral imaging. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 320:124579. [PMID: 38850824 DOI: 10.1016/j.saa.2024.124579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/10/2024]
Abstract
Among the severe foodborne illnesses, listeriosis resulting from the pathogen Listeria monocytogenes exhibits one of the highest fatality rates. This study investigated the application of near infrared hyperspectral imaging (NIR-HSI) for the classification of three L. monocytogenes serotypes namely serotype 4b, 1/2a and 1/2c. The bacteria were cultured on Brain Heart Infusion agar, and NIR hyperspectral images were captured in the spectral range 900-2500 nm. Different pre-processing methods were applied to the raw spectra and principal component analysis was used for data exploration. Classification was achieved with partial least squares discriminant analysis (PLS-DA). The PLS-DA results revealed classification accuracies exceeding 80 % for all the bacterial serotypes for both training and test set data. Based on validation data, sensitivity values for L. monocytogenes serotype 4b, 1/2a and 1/2c were 0.69, 0.80 and 0.98, respectively when using full wavelength data. The reduced wavelength model had sensitivity values of 0.65, 0.85 and 0.98 for serotype 4b, 1/2a and 1/2c, respectively. The most relevant bands for serotype discrimination were identified to be around 1490 nm and 1580-1690 nm based on both principal component loadings and variable importance in projection scores. The outcomes of this study demonstrate the feasibility of utilizing NIR-HSI for detecting and classifying L. monocytogenes serotypes on growth media.
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Affiliation(s)
- Rumbidzai T Matenda
- Department of Food Science, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7602, South Africa
| | - Diane Rip
- Department of Food Science, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7602, South Africa
| | - Juan A Fernández Pierna
- Quality and authentication of products Unit, Knowledge and valorization of agricultural products Department, Walloon Agricultural Research Centre (CRA-W), Chaussée de Namur,24, 5030 Gembloux, Belgium
| | - Vincent Baeten
- Quality and authentication of products Unit, Knowledge and valorization of agricultural products Department, Walloon Agricultural Research Centre (CRA-W), Chaussée de Namur,24, 5030 Gembloux, Belgium
| | - Paul J Williams
- Department of Food Science, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7602, South Africa.
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Osborne M, Fubara A, Ó Cinnéide E, Coughlan AY, Wolfe KH. WHO elements - A new category of selfish genetic elements at the borderline between homing elements and transposable elements. Semin Cell Dev Biol 2024; 163:2-13. [PMID: 38664119 DOI: 10.1016/j.semcdb.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 05/26/2024]
Abstract
Homing genetic elements are a form of selfish DNA that inserts into a specific target site in the genome and spreads through the population by a process of biased inheritance. Two well-known types of homing element, called inteins and homing introns, were discovered decades ago. In this review we describe WHO elements, a newly discovered type of homing element that constitutes a distinct third category but is rare, having been found only in a few yeast species so far. WHO elements are inferred to spread using the same molecular homing mechanism as inteins and introns: they encode a site-specific endonuclease that cleaves the genome at the target site, making a DNA break that is subsequently repaired by copying the element. For most WHO elements, the target site is in the glycolytic gene FBA1. WHO elements differ from inteins and homing introns in two fundamental ways: they do not interrupt their host gene (FBA1), and they occur in clusters. The clusters were formed by successive integrations of different WHO elements into the FBA1 locus, the result of an 'arms race' between the endonuclease and its target site. We also describe one family of WHO elements (WHO10) that is no longer specifically associated with the FBA1 locus and instead appears to have become transposable, inserting at random genomic sites in Torulaspora globosa with up to 26 copies per strain. The WHO family of elements is therefore at the borderline between homing genetic elements and transposable elements.
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Affiliation(s)
- Matthieu Osborne
- Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Athaliah Fubara
- Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Eoin Ó Cinnéide
- Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Aisling Y Coughlan
- Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Kenneth H Wolfe
- Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland.
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44
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Zhu L, Long P, Hu M, Wang L, Shao Y, Cheng S, Dong X, He Y. Insight into selenium biofortification and the selenite metabolic mechanism of Monascus ruber M7. Food Chem 2024; 455:139740. [PMID: 38843715 DOI: 10.1016/j.foodchem.2024.139740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 05/09/2024] [Accepted: 05/17/2024] [Indexed: 07/10/2024]
Abstract
Monascus species are functional fermentation fungi with great potential for selenium (Se) supplementation. This study investigated the effects of Se bio-fortification on the growth, morphology, and biosynthesis of Monascus ruber M7. The results demonstrated a significant increase in the yield of orange and red Monascus pigments (MPs) in red yeast rice (RYR) by 38.52% and 36.57%, respectively, under 20 μg/mL of selenite pressure. Meanwhile, the production of citrinin (CIT), a mycotoxin, decreased from 244.47 μg/g to 175.01 μg/g. Transcriptome analysis revealed significant upregulation of twelve genes involved in MPs biosynthesis, specifically MpigE, MpigF, and MpigN, and downregulation of four genes (mrr3, mrr4, mrr7, and mrr8) associated with CIT biosynthesis. Additionally, three genes encoding cysteine synthase cysK (Log2FC = 1.6), methionine synthase metH (Log2FC = 2.2), and methionyl-tRNA synthetase metG (Log2FC = 1.8) in selenocompound metabolism showed significantly upregulated. These findings provide insights into Se biotransformation and metabolism in filamentous fungi.
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Affiliation(s)
- Lisha Zhu
- National R&D Center for Se-rich Agricultural Products Processing, Hubei Engineering Research Center for Deep Processing of Green Se-rich Agricultural Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, PR China; Key Laboratory for Deep Processing of Major Grain and Oil, Ministry of Education, Hubei Key Laboratory for Processing and Transformation of Agricultural Products, School of Food Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, PR China
| | - Pengcheng Long
- National R&D Center for Se-rich Agricultural Products Processing, Hubei Engineering Research Center for Deep Processing of Green Se-rich Agricultural Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, PR China
| | - Man Hu
- National R&D Center for Se-rich Agricultural Products Processing, Hubei Engineering Research Center for Deep Processing of Green Se-rich Agricultural Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, PR China
| | - Liling Wang
- College of Food Science and Engineering, Tarim University, Alar 843300, PR China
| | - Yanchun Shao
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Shuiyuan Cheng
- National R&D Center for Se-rich Agricultural Products Processing, Hubei Engineering Research Center for Deep Processing of Green Se-rich Agricultural Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, PR China
| | - Xingxing Dong
- National R&D Center for Se-rich Agricultural Products Processing, Hubei Engineering Research Center for Deep Processing of Green Se-rich Agricultural Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, PR China
| | - Yi He
- National R&D Center for Se-rich Agricultural Products Processing, Hubei Engineering Research Center for Deep Processing of Green Se-rich Agricultural Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, PR China; Key Laboratory for Deep Processing of Major Grain and Oil, Ministry of Education, Hubei Key Laboratory for Processing and Transformation of Agricultural Products, School of Food Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, PR China.
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45
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Lembo A, Molinaro A, De Castro C, Berti F, Biagini M. Impact of glycosylation on viral vaccines. Carbohydr Polym 2024; 342:122402. [PMID: 39048237 DOI: 10.1016/j.carbpol.2024.122402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/24/2024] [Accepted: 06/11/2024] [Indexed: 07/27/2024]
Abstract
Glycosylation is the most prominent modification important for vaccines and its specific pattern depends on several factors that need to be considered when developing a new biopharmaceutical. Tailor-made glycosylation can be exploited to develop more effective and safer vaccines; for this reason, a deep understanding of both glycoengineering strategies and glycans structures and functions is required. In this review we discuss the recent advances concerning glycoprotein expression systems and the explanation of glycans immunomodulation mechanisms. Furthermore, we highlight how glycans tune the immunological properties among different vaccines platforms (whole virus, recombinant protein, nucleic acid), also comparing commercially available formulations and describing the state-of-the-art analytical technologies for glycosylation analysis. The whole review stresses the aspect of glycoprotein glycans as a potential tool to overcome nowadays medical needs in vaccine field.
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Affiliation(s)
- Antonio Lembo
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy; GSK, Siena, Italy
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Cristina De Castro
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy.
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46
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Zhao Y, Liu Y, Cao S, Hao Q, Liu C, Li Y. Anaerobic oxidation of methane driven by different electron acceptors: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174287. [PMID: 38945238 DOI: 10.1016/j.scitotenv.2024.174287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 05/31/2024] [Accepted: 06/23/2024] [Indexed: 07/02/2024]
Abstract
Methane, the most significant reduced form of carbon on Earth, acts as a crucial fuel and greenhouse gas. Globally, microbial methane sinks encompass both aerobic oxidation of methane (AeOM), conducted by oxygen-utilizing methanotrophs, and anaerobic oxidation of methane (AOM), performed by anaerobic methanotrophs employing various alternative electron acceptors. These electron acceptors involved in AOM include sulfate, nitrate/nitrite, humic substances, and diverse metal oxides. The known anaerobic methanotrophic pathways comprise the internal aerobic oxidation pathway found in NC10 bacteria and the reverse methanogenesis pathway utilized by anaerobic methanotrophic archaea (ANME). Diverse anaerobic methanotrophs can perform AOM independently or in cooperation with symbiotic partners through several extracellular electron transfer (EET) pathways. AOM has been documented in various environments, including seafloor methane seepages, coastal wetlands, freshwater lakes, soils, and even extreme environments like hydrothermal vents. The environmental activities of AOM processes, driven by different electron acceptors, primarily depend on the energy yields, availability of electron acceptors, and environmental adaptability of methanotrophs. It has been suggested that different electron acceptors driving AOM may occur across a wider range of habitats than previously recognized. Additionally, it is proposed that methanotrophs have evolved flexible metabolic strategies to adapt to complex environmental conditions. This review primarily focuses on AOM, driven by different electron acceptors, discussing the associated reaction mechanisms and the habitats where these processes are active. Furthermore, it emphasizes the pivotal role of AOM in mitigating methane emissions.
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Affiliation(s)
- Yuewen Zhao
- Fujian Provincial Key Laboratory of Water Cycling and Eco-Geological Processes, Xiamen 361021, China; Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang 050061, China
| | - Yaci Liu
- Fujian Provincial Key Laboratory of Water Cycling and Eco-Geological Processes, Xiamen 361021, China; Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang 050061, China.
| | - Shengwei Cao
- Fujian Provincial Key Laboratory of Water Cycling and Eco-Geological Processes, Xiamen 361021, China; Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang 050061, China
| | - Qichen Hao
- Fujian Provincial Key Laboratory of Water Cycling and Eco-Geological Processes, Xiamen 361021, China; Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang 050061, China
| | - Chunlei Liu
- Fujian Provincial Key Laboratory of Water Cycling and Eco-Geological Processes, Xiamen 361021, China; Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang 050061, China
| | - Yasong Li
- Fujian Provincial Key Laboratory of Water Cycling and Eco-Geological Processes, Xiamen 361021, China; Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang 050061, China.
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47
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Yang Y, Shen L, Jin Y, Bai Y, Wang S, Zhao X. Active role of iron-dependent AOM in paddy fields under different long-term fertilizer management schemes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174175. [PMID: 38908588 DOI: 10.1016/j.scitotenv.2024.174175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 06/10/2024] [Accepted: 06/19/2024] [Indexed: 06/24/2024]
Abstract
Iron-dependent anaerobic oxidation of methane (iron-AOM) has recently been reported to occur in paddy soils, but its actual role and regulation remain unclear. Here, we confirmed the occurrence of iron-AOM at different layers of paddy soils (0-10 cm, 10-20 cm, and 30-40 cm) across tillering, elongation, flowering, and ripening periods under three long-term fertilizer management schemes (CK-unamended, CF-chemical fertilizer, and CFS-chemical fertilizer with straw). The iron-AOM activity contributed 41 % to total AOM, which was greater than that of nitrite- (32 %) and nitrate-AOM (27 %). The iron-AOM activity varied significantly with soil layers, growth periods and fertilizer types, with layer being the most important variable. Soil moisture content and organic carbon content were most significant influencing factors on the AOM activity, and a Candidatus Methanoperedens ferrireducens-like lineage potentially catalyzed iron-AOM. Our results suggest that iron-AOM has an important potential for mitigating methane emissions from rice paddies.
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Affiliation(s)
- Yuling Yang
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Lidong Shen
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China.
| | - Yuhan Jin
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Yanan Bai
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Shuwei Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Changshu National Agro-Ecosystem Observation and Research Station, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xu Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Changshu National Agro-Ecosystem Observation and Research Station, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
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48
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Brtnicky M, Pecina V, Kucerik J, Hammerschmiedt T, Mustafa A, Kintl A, Sera J, Koutny M, Baltazar T, Holatko J. Biodegradation of poly-3-hydroxybutyrate after soil inoculation with microbial consortium: Soil microbiome and plant responses to the changed environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174328. [PMID: 38945229 DOI: 10.1016/j.scitotenv.2024.174328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 05/31/2024] [Accepted: 06/25/2024] [Indexed: 07/02/2024]
Abstract
Biodegradable plastics play a vital role in addressing global plastics disposal challenges. Poly-3-hydroxybutyrate (P3HB) is a biodegradable bacterial intracellular storage polymer with substantial usage potential in agriculture. Poly-3-hydroxybutyrate and its degradation products are non-toxic; however, previous studies suggest that P3HB biodegradation negatively affects plant growth because the microorganisms compete with plants for nutrients. One possible solution to this issue could be inoculating soil with a consortium of plant growth-promoting and N-fixing microorganisms. To test this hypothesis, we conducted a pot experiment using lettuce (Lactuca sativa L. var. capitata L.) grown in soil amended with two doses (1 % and 5 % w/w) of P3HB and microbial inoculant (MI). We tested five experimental variations: P3HB 1 %, P3HB 1 % + MI, P3HB 5 %, P3HB 5 % + MI, and MI, to assess the impact of added microorganisms on plant growth and P3HB biodegradation. The efficient P3HB degradation, which was directly dependent on the amount of bioplastics added, was coupled with the preferential utilization of P3HB as a carbon (C) source. Due to the increased demand for nutrients in P3HB-amended soil by microbial degraders, respiration and enzyme activities were enhanced. This indicated an increased mineralisation of C as well as nitrogen (N), sulphur (S), and phosphorus (P). Microbial inoculation introduced specific bacterial taxa that further improved degradation efficiency and nutrient turnover (N, S, and P) in P3HB-amended soil. Notably, soil acidification related to P3HB was not the primary factor affecting plant growth inhibition. However, despite plant growth-promoting rhizobacteria and N2-fixing microorganisms originating from MI, plant biomass yield remained limited, suggesting that these microorganisms were not entirely successful in mitigating the growth inhibition caused by P3HB.
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Affiliation(s)
- Martin Brtnicky
- Institute of Chemistry and Technology of Environmental Protection, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00 Brno, Czech Republic; Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Vaclav Pecina
- Institute of Chemistry and Technology of Environmental Protection, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00 Brno, Czech Republic; Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Jiri Kucerik
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic.
| | - Tereza Hammerschmiedt
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Adnan Mustafa
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Antonin Kintl
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic; Agricultural Research, Ltd., 664 41 Troubsko, Czech Republic
| | - Jana Sera
- Department of Environmental Protection Engineering, Faculty of Technology, Tomas Bata University in Zlin, Nad Ovcirnou 3685, 760 01 Zlin, Czech Republic
| | - Marek Koutny
- Department of Environmental Protection Engineering, Faculty of Technology, Tomas Bata University in Zlin, Nad Ovcirnou 3685, 760 01 Zlin, Czech Republic
| | - Tivadar Baltazar
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Jiri Holatko
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
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Yuan XQ, Liu YY, Wang SC, Lu YQ, Li YJ, Chen JQ, Duan CQ. Trifolium repens L. recruits root-associated Microbacterium species to adapt to heavy metal stress in an abandoned Pb-Zn mining area. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174057. [PMID: 38914340 DOI: 10.1016/j.scitotenv.2024.174057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 06/14/2024] [Accepted: 06/14/2024] [Indexed: 06/26/2024]
Abstract
Root-associated microbiota provide great fitness to hosts under environmental stress. However, the underlying microecological mechanisms controlling the interaction between heavy metal-stressed plants and the microbiota are poorly understood. In this study, we screened and isolated representative amplicon sequence variants (strain M4) from rhizosphere soil samples of Trifolium repens L. growing in areas with high concentrations of heavy metals. To investigate the microecological mechanisms by which T. repens adapts to heavy metal stress in abandoned mining areas, we conducted potting experiments, bacterial growth promotion experiments, biofilm formation experiments, and chemotaxis experiments. The results showed that high concentrations of heavy metals significantly altered the rhizosphere bacterial community structure of T. repens and significantly enriched Microbacterium sp. Strain M4 was demonstrated to significantly increased the biomass and root length of T. repens under heavy metal stress. Additionally, L-proline and stigmasterol could promote bacterial growth and biofilm formation and induce chemotaxis for strain M4, suggesting that they are key rhizosphere secretions of T. repens for Microbacterium sp. recruitment. Our results suggested that T. repens adapted the heavy metal stress by reshaping rhizosphere secretions to modify the rhizosphere microbiota.
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Affiliation(s)
- Xin-Qi Yuan
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments & School of Ecology and Environmental Sciences, Yunnan University, Kunming 650500, China; Central Yunnan Field Scientific Station for Restoration of Ecological Function & Yunnan International Joint Research Center of Plateau Lake Ecological Restoration and Watershed Management, Yunnan Think Tank for Ecological Civilization Construction, Yunnan University, Kunming 650091, China
| | - Yi-Yi Liu
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments & School of Ecology and Environmental Sciences, Yunnan University, Kunming 650500, China; Southwestern United Graduate School & Institute of International Rivers and Eco-security, Yunnan University, Kunming 650500, China
| | - Si-Chen Wang
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments & School of Ecology and Environmental Sciences, Yunnan University, Kunming 650500, China; Central Yunnan Field Scientific Station for Restoration of Ecological Function & Yunnan International Joint Research Center of Plateau Lake Ecological Restoration and Watershed Management, Yunnan Think Tank for Ecological Civilization Construction, Yunnan University, Kunming 650091, China
| | - Ya-Qi Lu
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments & School of Ecology and Environmental Sciences, Yunnan University, Kunming 650500, China; Southwestern United Graduate School & Institute of International Rivers and Eco-security, Yunnan University, Kunming 650500, China
| | - Yin-Jie Li
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments & School of Ecology and Environmental Sciences, Yunnan University, Kunming 650500, China; Central Yunnan Field Scientific Station for Restoration of Ecological Function & Yunnan International Joint Research Center of Plateau Lake Ecological Restoration and Watershed Management, Yunnan Think Tank for Ecological Civilization Construction, Yunnan University, Kunming 650091, China
| | - Jin-Quan Chen
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments & School of Ecology and Environmental Sciences, Yunnan University, Kunming 650500, China; Southwestern United Graduate School & Institute of International Rivers and Eco-security, Yunnan University, Kunming 650500, China.
| | - Chang-Qun Duan
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments & School of Ecology and Environmental Sciences, Yunnan University, Kunming 650500, China; Central Yunnan Field Scientific Station for Restoration of Ecological Function & Yunnan International Joint Research Center of Plateau Lake Ecological Restoration and Watershed Management, Yunnan Think Tank for Ecological Civilization Construction, Yunnan University, Kunming 650091, China; Southwestern United Graduate School & Institute of International Rivers and Eco-security, Yunnan University, Kunming 650500, China.
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Liu Q, Li X, Wu M, Huang H, Chen Y. N 2O recovery from wastewater and flue gas via microbial denitrification: Processes and mechanisms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174231. [PMID: 38917909 DOI: 10.1016/j.scitotenv.2024.174231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/06/2024] [Accepted: 06/21/2024] [Indexed: 06/27/2024]
Abstract
Nitrous oxide (N2O) is increasingly regarded as a significant greenhouse gas implicated in global warming and the depletion of the ozone layer, yet it is also recognized as a valuable resource. This paper comprehensively reviews innovative microbial denitrification techniques for recovering N2O from nitrogenous wastewater and flue gas. Critical analysis is carried out on cutting-edge processes such as the coupled aerobic-anoxic nitrous decomposition operation (CANDO) process, semi-artificial photosynthesis, and the selective utilization of microbial strains, as well as flue gas absorption coupled with heterotrophic/autotrophic denitrification. These processes are highlighted for their potential to facilitate denitrification and enhance the recovery rate of N2O. The review integrates feasible methods for process control and optimization, and presents the underlying mechanisms for N2O recovery through denitrification, primarily achieved by suppressing nitrous oxide reductase (Nos) activity and intensifying competition for electron donors. The paper concludes by recognizing the shortcomings in existing technologies and proposing future research directions, with an emphasis on prioritizing the collection and utilization of N2O while considering environmental sustainability and economic feasibility. Through this review, we aim to inspire interest in the recovery and utilization of N2O, as well as the development and application of related technologies.
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Affiliation(s)
- Qimeng Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Xinyi Li
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Meirou Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Haining Huang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; The Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, East China Normal University, Shanghai, China.
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China.
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